PMID-sentid	Pub_year	Sent_text	compound_name	comp_offset	prot_official_name	organism	prot_offset
33612899-5	2021	A compound hit (BBB_26580140) was stand out in the screening process, as opposed to the control, as a potential inhibitor of SARS-CoV-2 MPro based on a combined approach of SBVS, drug likeness and lead likeness annotations, pharmacokinetics, molecular dynamics (MD) simulations, and end point MM-PBSA binding free energy methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	296-300	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	136-140
34013346-6	2021	According to the result of MM-PBSA binding free energy calculations, we found that V367F and N354D/D364Y mutant types showed enhanced binding affinities with hACE2 compared to the prototype.	poly(tetramethylene succinate-co-tetramethylene adipate)	30-34	angiotensin converting enzyme 2	Homo sapiens	158-163
98868-1	1978	Bovine Serum Albumin solutions (BSA) have been chemically polymerized to give solutions (PBSA) with superior serological properties.	poly(tetramethylene succinate-co-tetramethylene adipate)	89-93	albumin	Bos taurus	7-20
33612899-7	2021	A set of three compounds (SCHEMBL12616233, SCHEMBL18616095, and SCHEMBL20148701), based on their binding affinity for MPro, was selected and analyzed using extensive MD simulation, hydrogen bond profiling, MM-PBSA, and WaterSwap binding free energy techniques.	poly(tetramethylene succinate-co-tetramethylene adipate)	209-213	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	118-122
33684714-12	2021	In addition, the MM-PBSA calculations ascribed the lowest binding free energy to the 7d-CDK2 complex (-323.69 +- 15.17 kJ/mol).	poly(tetramethylene succinate-co-tetramethylene adipate)	20-24	cyclin dependent kinase 2	Homo sapiens	88-92
33686514-0	2022	CHK1 kinase inhibition: identification of allosteric hits using MD simulations, pharmacophore modeling, docking and MM-PBSA calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	119-123	checkpoint kinase 1	Homo sapiens	0-4
33248341-6	2021	These attempts yielded a small peptide library, which was further investigated for peptide affinities towards C terminal of NFAT5 RHR through molecular docking, 50 ns and 250 ns molecular dynamics simulations, followed by estimation of MM-PBSA based relative binding free energies.	poly(tetramethylene succinate-co-tetramethylene adipate)	239-243	nuclear factor of activated T cells 5	Homo sapiens	124-129
33618628-3	2021	After the initial virtual screening of a number of bioactive flavonoids, the binding affinity of three compounds - Naringin, Naringenin and Amentoflavone - at the active site of Mpro was investigated through MD Simulations, MM-PBSA and DFT Binding Energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	227-231	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	178-182
33248341-0	2021	Structure based peptide design, molecular dynamics and MM-PBSA studies for targeting C terminal dimerization of NFAT5 DNA binding domain.	poly(tetramethylene succinate-co-tetramethylene adipate)	58-62	nuclear factor of activated T cells 5	Homo sapiens	112-117
33583350-6	2021	Perceptibly, the combined "anti-HIV drug and phyto-flavonoid" docking complex has actively interacted with eight strong H-bonds with stability, briefly elucidated through RMRD-, RMSF- Rg-plots and MM/PBSA-binding energy calculation during 100 ns than the individual against SARS-CoV-2-Mpro.	poly(tetramethylene succinate-co-tetramethylene adipate)	200-204	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	285-289
33671607-10	2021	The MM-PBSA calculations revealed that compounds 4, 5, 7 and 9 possess highest affinity for TNF-alpha; 8, 11, 13-15 exhibited moderate affinities, while compound 10 showed weaker binding affinity with TNF-alpha.	poly(tetramethylene succinate-co-tetramethylene adipate)	7-11	tumor necrosis factor	Homo sapiens	92-101
33173250-10	2021	A rich pattern of hydrogen and hydrophobic interactions of the construct was observed with the TLR3 allowing stable binding of the construct at the docked site as predicted by the molecular dynamics simulation and MM-PBSA binding energies.	poly(tetramethylene succinate-co-tetramethylene adipate)	217-221	toll like receptor 3	Homo sapiens	95-99
31916502-0	2021	Molecular modeling studies of pyrrolo[2,3-d]pyrimidin-4-amine derivatives as JAK1 inhibitors based on 3D-QSAR, molecular docking, molecular dynamics (MD) and MM-PBSA calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	161-165	Janus kinase 1	Homo sapiens	77-81
31916502-12	2021	MM-PBSA based free energy calculations indicated that the designed compounds were able to form stable binding with JAK1 primarily through electrostatic interactions and van der Waal interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	Janus kinase 1	Homo sapiens	115-119
33161767-8	2021	High negative binding free energy of identified four compounds calculated through MM-PBSA approach demonstrated a strong binding affinity towards the Lyn protein.	poly(tetramethylene succinate-co-tetramethylene adipate)	85-89	LYN proto-oncogene, Src family tyrosine kinase	Homo sapiens	150-153
33427075-11	2021	In the calculations of free energy MM/PBSA, the molecule ZINC408709 DeltaGbind value has a higher affinity to celecoxib and rofecoxib COX-2.	poly(tetramethylene succinate-co-tetramethylene adipate)	38-42	prostaglandin-endoperoxide synthase 2	Homo sapiens	134-139
32916377-10	2020	Eventually, the MM-PBSA results showed the full-length model had a stronger binding free energy (almost 5-fold) than the RBD structure model of SARS-CoV2 S spike protein complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	19-23	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	156-161
33143552-0	2022	Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	124-128	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	45-49
32851579-7	2020	Overall, the performance of MM/PBSA rescoring in improving virtual screening enrichment obtained from docking of the GPCR-Bench dataset was found to be relatively modest and target-specific, highlighting the need for validation of MM/PBSA-based protocols prior to prospective use.	poly(tetramethylene succinate-co-tetramethylene adipate)	31-35	C-X-C motif chemokine receptor 6	Homo sapiens	117-121
32462752-5	2020	MM/PBSA produced r values ranging from 0.410 - 0.688 for the CB1 agonists and 0.420 - 0.678 for the CB1 antagonists depending on the simulation parameters, which were modestly better than correlations obtained using docking scores.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	cannabinoid receptor 1	Homo sapiens	61-64
32462752-5	2020	MM/PBSA produced r values ranging from 0.410 - 0.688 for the CB1 agonists and 0.420 - 0.678 for the CB1 antagonists depending on the simulation parameters, which were modestly better than correlations obtained using docking scores.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	cannabinoid receptor 1	Homo sapiens	100-103
32851579-7	2020	Overall, the performance of MM/PBSA rescoring in improving virtual screening enrichment obtained from docking of the GPCR-Bench dataset was found to be relatively modest and target-specific, highlighting the need for validation of MM/PBSA-based protocols prior to prospective use.	poly(tetramethylene succinate-co-tetramethylene adipate)	234-238	C-X-C motif chemokine receptor 6	Homo sapiens	117-121
32569626-10	2020	MM/PBSA binding free energy for malvidin-3-glucoside to PTP1B was found to be higher than other complexes mediated by Van der Waals energy rather than electrostatic interaction for the other two inhibitors (-80.32 +- 1.25 > -40.64 +- 1.43 > -21.63+-1.73 kcal/mol) respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	protein tyrosine phosphatase non-receptor type 1	Homo sapiens	56-61
32569626-4	2020	Enzyme kinetics identified the mode of inhibition, while dynamics, stability and binding mechanisms of PTP1B-ligand complex were investigated through molecular modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation.	poly(tetramethylene succinate-co-tetramethylene adipate)	224-228	protein tyrosine phosphatase non-receptor type 1	Homo sapiens	103-108
32830209-10	2020	The MM-PBSA results revealed the binding of REF to chain A of the Abeta oligomer.	poly(tetramethylene succinate-co-tetramethylene adipate)	7-11	amyloid beta precursor protein	Homo sapiens	66-71
32070031-8	2020	The docking results were complemented by all-atom molecular dynamics simulation for 100 ns, followed by MM/PBSA, and principal component analysis to investigate the conformational changes, stability, and interaction mechanism of SGK1 in-complex with the selected compound ZINC00319000.	poly(tetramethylene succinate-co-tetramethylene adipate)	107-111	serum/glucocorticoid regulated kinase 1	Homo sapiens	229-233
32752079-13	2020	Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM/PBSA binding free energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	209-213	dihydrofolate reductase	Homo sapiens	121-126
30955452-8	2020	Strong binding affinity was found for all molecules toward the EGFR which was substantiated by the binding energy calculation using the MM-PBSA approach.	poly(tetramethylene succinate-co-tetramethylene adipate)	139-143	epidermal growth factor receptor	Homo sapiens	63-67
30963817-11	2020	Further, the stability of the molecule has been confirmed from the MD simulation and the binding free energy of the indirubin-3-monoxime-GSK3beta complex has been determined using MM/PBSA method to validate the binding affinity of indirubin-3-monoxime.	poly(tetramethylene succinate-co-tetramethylene adipate)	183-187	glycogen synthase kinase 3 beta	Homo sapiens	137-145
32196303-0	2020	Prediction of the binding affinities and selectivity for CB1 and CB2 ligands using homology modeling, molecular docking, molecular dynamics simulations, and MM-PBSA binding free energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	160-164	cannabinoid receptor 1	Homo sapiens	57-60
32196303-0	2020	Prediction of the binding affinities and selectivity for CB1 and CB2 ligands using homology modeling, molecular docking, molecular dynamics simulations, and MM-PBSA binding free energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	160-164	cannabinoid receptor 2	Homo sapiens	65-68
32043094-0	2020	Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method.	poly(tetramethylene succinate-co-tetramethylene adipate)	36-40	BCL2 apoptosis regulator	Homo sapiens	104-109
29310523-5	2019	In this study, we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3beta through docking, molecular dynamics, binding energy (MM-PBSA).	poly(tetramethylene succinate-co-tetramethylene adipate)	171-175	beta-secretase 1	Homo sapiens	94-100
31265936-6	2019	The binding energy obtained from Molecular Mechanics- Poisson Boltzman Surface Area, MM-PBSA method, revealed that Vitamins D3 and E have good affinity to bind to the insulin and vitamin E has higher binding energy (-46 kj/mol) by engaging more residues in binding site.	poly(tetramethylene succinate-co-tetramethylene adipate)	88-92	insulin	Homo sapiens	167-174
30989572-3	2019	Binding of four putative inhibitors of kallikrein-8 is investigated through molecular dynamics simulation and ligand binding energy evaluation with two methods (MM/PBSA and WaterSwap).	poly(tetramethylene succinate-co-tetramethylene adipate)	164-168	kallikrein related peptidase 8	Homo sapiens	39-51
30989574-0	2019	Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	G protein-coupled receptor 166 pseudogene	Homo sapiens	84-88
30989574-3	2019	In this study, we systematically assessed the performance of MM/PBSA in predicting experimental binding free energies using twenty Class A GPCR crystal structures and 934 known ligands.	poly(tetramethylene succinate-co-tetramethylene adipate)	64-68	G protein-coupled receptor 166 pseudogene	Homo sapiens	139-143
30989574-5	2019	MM/PBSA provided better predictions of binding free energies compared to docking scores in eight out of the twenty GPCR targets while performing worse for four targets.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	G protein-coupled receptor 166 pseudogene	Homo sapiens	115-119
30989574-8	2019	In conclusion, while MM/PBSA remains a valuable tool for GPCR structure-based drug design, its performance in predicting the binding free energies of GPCR ligands remains highly system-specific as demonstrated in a subset of twenty Class A GPCRs, and validation of MM/PBSA-based methods for each individual case is recommended before prospective use.	poly(tetramethylene succinate-co-tetramethylene adipate)	268-272	G protein-coupled receptor 166 pseudogene	Homo sapiens	150-154
30856053-14	2020	Abbreviations SA Saccharin SSA Sodium Saccharin Pp53g promoter of human p53 gene MD Molecular dynamics RMSD Root-mean-square deviation RMSF Root-mean-square fluctuation Rg Radius of Gyration SASA Solvent-Accessible Surface Area ADI Acceptable daily intake MM/PBSA Molecular Mechanics/Poisson-Boltzmann Surface Area Communicated by Ramaswamy H. Sarma.	poly(tetramethylene succinate-co-tetramethylene adipate)	259-263	tumor protein p53	Homo sapiens	49-52
31524891-0	2019	Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy.	poly(tetramethylene succinate-co-tetramethylene adipate)	111-115	ALK receptor tyrosine kinase	Homo sapiens	49-75
30296922-7	2019	MM/PBSA binding free energy study revealed that non-polar solvation (van der Waals and electrostatic) energy subsidizes significantly to the total binding energy, and the polar solvation energy opposes the binding agonists to GLP-1R.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	glucagon like peptide 1 receptor	Homo sapiens	226-232
31069854-3	2019	In this study, a design strategy combining docking, molecular dynamics, and MM-PBSA is presented, to predict the catalytically active site of glutathione peroxidase (GPx) on the allosteric domain of Rn.	poly(tetramethylene succinate-co-tetramethylene adipate)	79-83	recoverin	Homo sapiens	199-201
29310523-5	2019	In this study, we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3beta through docking, molecular dynamics, binding energy (MM-PBSA).	poly(tetramethylene succinate-co-tetramethylene adipate)	171-175	glycogen synthase kinase 3 beta	Homo sapiens	105-114
29342447-7	2018	Compound 31 had good intermolecular interaction with PTK in the molecular docking studies, this ligand-enzyme complex was found to stable in the MM-PBSA study over 100 ns.	poly(tetramethylene succinate-co-tetramethylene adipate)	148-152	EPH receptor A8	Homo sapiens	53-56
29758466-4	2018	Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands.	poly(tetramethylene succinate-co-tetramethylene adipate)	251-255	CREB binding protein	Homo sapiens	111-117
29738770-5	2018	A ligand-binding simulation model using the MM-PBSA method indicates that both of the five-amino-acid sequence elements of AtS6K1 and AtATG13 have strong probability of making stable interface with the Raptor binding pocket, corroborating our proposition for this element as the plant TOS motif.	poly(tetramethylene succinate-co-tetramethylene adipate)	47-51	protein-serine kinase 1	Arabidopsis thaliana	123-129
29738770-5	2018	A ligand-binding simulation model using the MM-PBSA method indicates that both of the five-amino-acid sequence elements of AtS6K1 and AtATG13 have strong probability of making stable interface with the Raptor binding pocket, corroborating our proposition for this element as the plant TOS motif.	poly(tetramethylene succinate-co-tetramethylene adipate)	47-51	Autophagy-related protein 13	Arabidopsis thaliana	134-141
30448921-8	2018	Determination of the MM/PBSA free energy indicated that the binding of DHP-8 to SIRT1 significantly increased the binding affinity of SIRT1 to its substrate p53-W as well as to NAD+.	poly(tetramethylene succinate-co-tetramethylene adipate)	24-28	dihydropyrimidinase	Homo sapiens	71-74
30448921-8	2018	Determination of the MM/PBSA free energy indicated that the binding of DHP-8 to SIRT1 significantly increased the binding affinity of SIRT1 to its substrate p53-W as well as to NAD+.	poly(tetramethylene succinate-co-tetramethylene adipate)	24-28	sirtuin 1	Homo sapiens	80-85
30448921-8	2018	Determination of the MM/PBSA free energy indicated that the binding of DHP-8 to SIRT1 significantly increased the binding affinity of SIRT1 to its substrate p53-W as well as to NAD+.	poly(tetramethylene succinate-co-tetramethylene adipate)	24-28	sirtuin 1	Homo sapiens	134-139
30448921-8	2018	Determination of the MM/PBSA free energy indicated that the binding of DHP-8 to SIRT1 significantly increased the binding affinity of SIRT1 to its substrate p53-W as well as to NAD+.	poly(tetramethylene succinate-co-tetramethylene adipate)	24-28	tumor protein p53	Homo sapiens	157-160
30031079-0	2018	MM-PBSA and per-residue decomposition energy studies on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	prostaglandin E synthase	Homo sapiens	145-182
30031079-8	2018	The results clearly show that MM-PBSA can act as a filter in virtual screening experiments and can play major role in facilitating various mPGES-1 drug discovery studies.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	prostaglandin E synthase	Mus musculus	139-146
30213978-4	2018	In addition, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method was applied to analyze the binding free energy decompositions of the CB1-ligand complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	72-76	cannabinoid receptor 1	Homo sapiens	154-157
29574142-0	2018	Exploring the interactions of EGFR with phosphorylated Mig6 by molecular dynamics simulations and MM-PBSA calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	101-105	epidermal growth factor receptor	Homo sapiens	30-34
29719770-0	2018	Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach.	poly(tetramethylene succinate-co-tetramethylene adipate)	112-116	lemur tyrosine kinase 3	Homo sapiens	48-53
29719770-8	2018	In addition, MM/PBSA calculations also confirmed the relative binding free energy of LMTK3-lead complexes in favor of the effective binding.	poly(tetramethylene succinate-co-tetramethylene adipate)	16-20	lemur tyrosine kinase 3	Homo sapiens	85-90
28817220-3	2017	In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA.	poly(tetramethylene succinate-co-tetramethylene adipate)	223-227	kallikrein related peptidase 14	Homo sapiens	14-19
29450111-6	2018	To clarify the reason, we performed molecular dynamics (MD) simulations for a complex of CPD-PHR or CRY-DASH with damaged double-stranded DNA (dsDNA) and estimated the binding free energy, DeltaGbind, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method.	poly(tetramethylene succinate-co-tetramethylene adipate)	309-313	MYC binding protein 2	Homo sapiens	93-96
29111719-1	2017	Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson-Boltzmann surface area (FMO+MM-PBSA) approach.	poly(tetramethylene succinate-co-tetramethylene adipate)	263-267	Pim-1 proto-oncogene, serine/threonine kinase	Homo sapiens	112-116
28427307-3	2018	The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32.LyP-1 complex in water has been shown by explicit water MD computations.	poly(tetramethylene succinate-co-tetramethylene adipate)	61-65	inhibitor of growth family member 2	Homo sapiens	117-120
28427307-3	2018	The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32.LyP-1 complex in water has been shown by explicit water MD computations.	poly(tetramethylene succinate-co-tetramethylene adipate)	61-65	protein tyrosine phosphatase non-receptor type 22	Homo sapiens	121-126
29546582-8	2018	Our simulation study showed that the A18-NA complex is as stable as the OTV-NA complex during the MD simulation of 50 ns through the analysis of RMSD, RMSF, total energy, hydrogen bonding, and MM/PBSA free energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	196-200	immunoglobulin kappa variable 2-29	Homo sapiens	37-40
29546582-8	2018	Our simulation study showed that the A18-NA complex is as stable as the OTV-NA complex during the MD simulation of 50 ns through the analysis of RMSD, RMSF, total energy, hydrogen bonding, and MM/PBSA free energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	196-200	neuraminidase 1	Homo sapiens	41-43
28707052-3	2018	Additionally, the binding free energy calculated by Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) is also revealed that electrostatic energy and polar solvation energy mainly made up the binding free energy of PTP1B-IRK complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	107-111	protein tyrosine phosphatase non-receptor type 1	Homo sapiens	225-230
28817220-3	2017	In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA.	poly(tetramethylene succinate-co-tetramethylene adipate)	223-227	serine peptidase inhibitor, Kunitz type 1	Homo sapiens	91-96
28024230-4	2017	The binding free energies predicted by MM-PBSA method showed that most compounds exhibited higher affinity than that of native ligand (4-anilinoquinazoline, DTQ) and the affinity of mono-H2PyP-AQ was about three times better than that of DTQ, indicating its potential to be advanced as a new CDK2 inhibitor.	poly(tetramethylene succinate-co-tetramethylene adipate)	42-46	cyclin dependent kinase 2	Homo sapiens	292-296
28810191-6	2017	Molecular Dynamic and Molecular Mechanics Poisson-Boltzmann Surface Area simulations (MM-PBSA) demonstrated that the ACE/BBP-BrachyNH2 complex showed lower binding and van der Wall energies than the ACE/des-Pro8-BPP-BrachyNH2 complex, therefore having better stability.	poly(tetramethylene succinate-co-tetramethylene adipate)	89-93	angiotensin I converting enzyme	Homo sapiens	117-120
28810191-6	2017	Molecular Dynamic and Molecular Mechanics Poisson-Boltzmann Surface Area simulations (MM-PBSA) demonstrated that the ACE/BBP-BrachyNH2 complex showed lower binding and van der Wall energies than the ACE/des-Pro8-BPP-BrachyNH2 complex, therefore having better stability.	poly(tetramethylene succinate-co-tetramethylene adipate)	89-93	transmembrane protein 158	Homo sapiens	121-124
28707627-5	2017	Second, BMP-2-encapsulated BSA microspheres were prepared through desolvation, and then were also decorated by PDA (pBSA-MS).	poly(tetramethylene succinate-co-tetramethylene adipate)	116-120	bone morphogenetic protein 2	Homo sapiens	8-13
28707627-7	2017	Bone marrow stromal cell cultures and in vivo implantation, showed that the pHA/pBSA (BMP-2) coatings can promote cell adhesion, proliferation, and benefited for osteoinductivity.	poly(tetramethylene succinate-co-tetramethylene adipate)	80-84	bone morphogenetic protein 2	Homo sapiens	86-91
28568844-0	2017	Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	76-80	beta-secretase 1	Homo sapiens	22-28
27760293-7	2016	Molecular docking together with molecular dynamics simulations and MM/PBSA methods were applied to gain insights into the binding modes and free energies of SOD1-flavonoid complexes at the molecule level.	poly(tetramethylene succinate-co-tetramethylene adipate)	70-74	superoxide dismutase 1	Homo sapiens	157-161
27056562-10	2017	In addition, binding free energy of the LMTK3-ligand complexes were calculated by MM/PBSA methods and results supported the strong binding in dynamic system.	poly(tetramethylene succinate-co-tetramethylene adipate)	85-89	lemur tyrosine kinase 3	Homo sapiens	40-45
25582663-0	2016	Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation.	poly(tetramethylene succinate-co-tetramethylene adipate)	130-134	angiotensin I converting enzyme	Homo sapiens	75-104
27507430-5	2016	The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC.	poly(tetramethylene succinate-co-tetramethylene adipate)	113-117	coagulation factor II, thrombin	Homo sapiens	4-12
28077888-5	2016	CONCLUSION: Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.	poly(tetramethylene succinate-co-tetramethylene adipate)	71-75	mitochondrially encoded cytochrome c oxidase I	Homo sapiens	252-257
28077888-5	2016	CONCLUSION: Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.	poly(tetramethylene succinate-co-tetramethylene adipate)	71-75	mitochondrially encoded cytochrome c oxidase II	Homo sapiens	326-331
27262595-6	2016	MM-PBSA per-residue energy decomposition identified important interactions of the compounds with specific TDP2 residues.	poly(tetramethylene succinate-co-tetramethylene adipate)	2-7	tyrosyl-DNA phosphodiesterase 2	Homo sapiens	106-110
27371933-0	2016	Binding mechanism of CDK5 with roscovitine derivatives based on molecular dynamics simulations and MM/PBSA methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	102-106	cyclin dependent kinase 5	Homo sapiens	21-25
27082784-7	2016	We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	154-158	CREB binding protein	Mus musculus	68-71
27082784-7	2016	We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	154-158	myeloblastosis oncogene	Mus musculus	72-77
27240358-2	2016	To elucidate the molecular mechanism of drug resistance associated with mutations (D30N, I50V, I54M, and V82A) and inhibitor (GRL-0519) complexes, we have performed five molecular dynamics (MD) simulations and calculated the binding free energies using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method.	poly(tetramethylene succinate-co-tetramethylene adipate)	312-316	nuclear receptor subfamily 3 group C member 1	Homo sapiens	126-129
26863418-0	2016	Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	122-126	MDM2 proto-oncogene	Homo sapiens	38-42
25582663-0	2016	Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation.	poly(tetramethylene succinate-co-tetramethylene adipate)	130-134	angiotensinogen	Homo sapiens	109-123
26362600-7	2015	Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation.	poly(tetramethylene succinate-co-tetramethylene adipate)	196-200	BCL2 antagonist/killer 1	Homo sapiens	120-129
25142337-3	2014	Detailed MM-PBSA calculations revealed that the binding free energies of the valmerin-19 to GSK3beta/CDK5 were calculated to be -12.60 +- 2.28 kcal mol(-1) and -11.85 +- 2.54 kcal mol(-1), respectively, indicating that valmerin-19 has the potential to act as a dual inhibitor of GSK3beta/CDK5.	poly(tetramethylene succinate-co-tetramethylene adipate)	12-16	glycogen synthase kinase 3 beta	Homo sapiens	92-100
26419972-10	2015	The stability and MM-PBSA binding energy of GRP78-inhibitor complexes as well as energetic contribution of individual residues was analyzed by 50 ns molecular dynamics run with GROMACS.	poly(tetramethylene succinate-co-tetramethylene adipate)	21-25	heat shock protein family A (Hsp70) member 5	Homo sapiens	44-49
25644934-6	2015	Notably, the binding free energies predicted by MM/GBSA or MM/PBSA based on the MD simulations for the docked poses give the highest correlation with the experimental data, highlighting the importance of the inclusion of receptor flexibility for the accurate predictions of the binding potencies for Type I1/2 inhibitors of ALK.	poly(tetramethylene succinate-co-tetramethylene adipate)	62-66	ALK receptor tyrosine kinase	Homo sapiens	324-327
25406390-7	2015	In an energetic analysis, the MM-PBSA (molecular mechanics Poisson-Boltzmann surface) energy decomposition revealed that the van der Waals interactions were the major driving force for the binding of the DFG-in and DFG-out compounds to Src and Abl, especially the hydrophobic interactions between ligands and residues Ala403/380, Asp404/381, and Phe405/382 in DFG-out Src and Abl complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	SRC proto-oncogene, non-receptor tyrosine kinase	Homo sapiens	236-239
25406390-7	2015	In an energetic analysis, the MM-PBSA (molecular mechanics Poisson-Boltzmann surface) energy decomposition revealed that the van der Waals interactions were the major driving force for the binding of the DFG-in and DFG-out compounds to Src and Abl, especially the hydrophobic interactions between ligands and residues Ala403/380, Asp404/381, and Phe405/382 in DFG-out Src and Abl complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	ABL proto-oncogene 1, non-receptor tyrosine kinase	Homo sapiens	244-247
25406390-7	2015	In an energetic analysis, the MM-PBSA (molecular mechanics Poisson-Boltzmann surface) energy decomposition revealed that the van der Waals interactions were the major driving force for the binding of the DFG-in and DFG-out compounds to Src and Abl, especially the hydrophobic interactions between ligands and residues Ala403/380, Asp404/381, and Phe405/382 in DFG-out Src and Abl complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	SRC proto-oncogene, non-receptor tyrosine kinase	Homo sapiens	368-371
25406390-7	2015	In an energetic analysis, the MM-PBSA (molecular mechanics Poisson-Boltzmann surface) energy decomposition revealed that the van der Waals interactions were the major driving force for the binding of the DFG-in and DFG-out compounds to Src and Abl, especially the hydrophobic interactions between ligands and residues Ala403/380, Asp404/381, and Phe405/382 in DFG-out Src and Abl complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	33-37	ABL proto-oncogene 1, non-receptor tyrosine kinase	Homo sapiens	376-379
26476847-6	2015	In MM-PBSA, a variety of EGFR structures have identically good performance in the scoring and ranking of known inhibitors, indicating that the choice of the receptor structure has little effect on the screening.	poly(tetramethylene succinate-co-tetramethylene adipate)	6-10	epidermal growth factor receptor	Homo sapiens	25-29
26578958-3	2015	The analysis of anti-VEGF/VEGFA complexes was carried out by means of protein-protein docking and molecular dynamics (MD) coupled to molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation.	poly(tetramethylene succinate-co-tetramethylene adipate)	188-192	vascular endothelial growth factor A	Homo sapiens	21-25
26578958-3	2015	The analysis of anti-VEGF/VEGFA complexes was carried out by means of protein-protein docking and molecular dynamics (MD) coupled to molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation.	poly(tetramethylene succinate-co-tetramethylene adipate)	188-192	vascular endothelial growth factor A	Homo sapiens	26-31
26578958-6	2015	Comparison of MM-PBSA predicted energy terms with experimental binding parameters reported in literature indicated that the high association rate (Kon) of aflibercept to VEGFA was consistent with high stabilizing electrostatic energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	17-21	vascular endothelial growth factor A	Homo sapiens	170-175
25662919-5	2015	We simulated two complexes of gamma-tubulin-GCP4 complex (we called dimer1 and dimer2) for 25 ns to obtain a stable complex and calculated the ensemble average of binding free energies of -158.82 and -170.19 kcal/mol for dimer1 and -79.53 and -101.50 kcal/mol for dimer2 using MM-PBSA and MM-GBSA methods, respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	280-284	tubulin gamma complex associated protein 4	Homo sapiens	44-48
25488424-9	2015	Binding energy (BE) calculation using MM/PBSA method from the TLR3- and TLR22-ligand complexes revealed an adequate binding affinity between TLR22-monomer and dsRNA as like as TLR3-dimer-dsRNA complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	41-45	toll-like receptor 3	Danio rerio	62-66
25488424-9	2015	Binding energy (BE) calculation using MM/PBSA method from the TLR3- and TLR22-ligand complexes revealed an adequate binding affinity between TLR22-monomer and dsRNA as like as TLR3-dimer-dsRNA complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	41-45	toll-like receptor 22	Danio rerio	72-77
25488424-9	2015	Binding energy (BE) calculation using MM/PBSA method from the TLR3- and TLR22-ligand complexes revealed an adequate binding affinity between TLR22-monomer and dsRNA as like as TLR3-dimer-dsRNA complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	41-45	toll-like receptor 22	Danio rerio	141-146
25488424-9	2015	Binding energy (BE) calculation using MM/PBSA method from the TLR3- and TLR22-ligand complexes revealed an adequate binding affinity between TLR22-monomer and dsRNA as like as TLR3-dimer-dsRNA complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	41-45	toll-like receptor 3	Danio rerio	176-180
25142337-3	2014	Detailed MM-PBSA calculations revealed that the binding free energies of the valmerin-19 to GSK3beta/CDK5 were calculated to be -12.60 +- 2.28 kcal mol(-1) and -11.85 +- 2.54 kcal mol(-1), respectively, indicating that valmerin-19 has the potential to act as a dual inhibitor of GSK3beta/CDK5.	poly(tetramethylene succinate-co-tetramethylene adipate)	12-16	cyclin dependent kinase 5	Homo sapiens	101-105
25060329-9	2014	Moreover, MM-PBSA calculations showed that the more efficient JDTic binding to kappa-OR compared to SalA (DeltaGJDTic = -31.6 kcal mol(-1), DeltaGSalA = -9.8 kcal mol(-1)) is attributed mostly to differences in electrostatic contributions.	poly(tetramethylene succinate-co-tetramethylene adipate)	13-17	opioid receptor kappa 1	Homo sapiens	79-87
24562912-6	2014	Molecular dynamics simulations and MM-PBSA calculations suggested that two of the inhibitors, compounds 32056 and 31674, could stably bind to the CPSF30-binding site with high binding free energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	38-42	cleavage and polyadenylation specific factor 4	Homo sapiens	146-152
24754906-11	2014	Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	73-77	cyclin dependent kinase 8	Homo sapiens	53-57
24754906-11	2014	Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	73-77	cyclin C	Homo sapiens	62-66
24754906-11	2014	Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	73-77	cyclin dependent kinase 8	Homo sapiens	175-179
24754906-11	2014	Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	73-77	cyclin C	Homo sapiens	180-184
24490903-3	2014	In the current work, we used ligand docking in combination with QM/MM-GBSA, MM-GBSA, and MM-PBSA rescoring to discriminate between active and inactive Myt1 kinase inhibitors.	poly(tetramethylene succinate-co-tetramethylene adipate)	92-96	protein kinase, membrane associated tyrosine/threonine 1	Homo sapiens	151-162
25098505-3	2014	We used the implicit Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method to estimate the free energies of binding for the phenyl based compound/ERRgamma systems.	poly(tetramethylene succinate-co-tetramethylene adipate)	76-80	estrogen related receptor gamma	Homo sapiens	160-168
24028418-8	2014	The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	6-11	islet amyloid polypeptide	Homo sapiens	62-68
24432790-3	2014	We have developed a protocol to include water molecules that mediate ligand-protein interactions as part of the protein structure in calculation of MM/PBSA binding energies (a method we refer to as water-MM/PBSA) for a series of JNK3 kinase inhibitors.	poly(tetramethylene succinate-co-tetramethylene adipate)	151-155	mitogen-activated protein kinase 10	Homo sapiens	229-233
24432790-3	2014	We have developed a protocol to include water molecules that mediate ligand-protein interactions as part of the protein structure in calculation of MM/PBSA binding energies (a method we refer to as water-MM/PBSA) for a series of JNK3 kinase inhibitors.	poly(tetramethylene succinate-co-tetramethylene adipate)	207-211	mitogen-activated protein kinase 10	Homo sapiens	229-233
24028418-8	2014	The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	6-11	islet amyloid polypeptide	Homo sapiens	70-76
23803191-2	2013	METHODS: The binding interaction of the candidate molecules binding gp120 and changes of the binding free energy were analyzed by MM-PBSA calculation.	poly(tetramethylene succinate-co-tetramethylene adipate)	133-137	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	68-73
23748247-4	2013	We described an approach that combines molecular docking, molecular dynamics, MM-PBSA calculations and conformational analysis to rationally predict piperazine derivatives binding mode with HIV-1 gp120.	poly(tetramethylene succinate-co-tetramethylene adipate)	81-85	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	196-201
23382875-10	2013	MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-alpha>BTC>EPR>EPG>AR.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	epidermal growth factor receptor	Homo sapiens	69-73
23382875-10	2013	MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-alpha>BTC>EPR>EPG>AR.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	transforming growth factor alpha	Homo sapiens	134-143
22568977-6	2012	RESULTS: Applying MM/PBSA methodology to different stoichiometric complexes of human LT-(TNFR1)n=1,2,3 the free energy of binding in these complexes has been estimated by single-trajectory and separate-trajectory methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	21-25	TNF receptor superfamily member 1A	Homo sapiens	89-94
22643974-8	2012	In addition, the MM-PBSA calculations reveal that the binding of these inhibitors to Aurora B kinase is mainly driven by van der Waals/nonpolar interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	20-24	aurora kinase B	Homo sapiens	85-93
23382805-4	2013	To elucidate the molecular basis of the small molecules interactions to inhibit the SIRT2 function we employed the molecular docking, molecular dynamics simulations, and the molecular mechanism Poisson-Boltzmann/surface area (MM-PBSA) calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	229-233	sirtuin 2	Homo sapiens	84-89
23382805-7	2013	In addition, the MM-PBSA calculations revealed that binding of inhibitors to SIRT2 is mainly driven by van der Waals/non-polar interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	20-24	sirtuin 2	Homo sapiens	77-82
21970461-1	2011	Using the recently solved crystal structure of the human adenosine A(2A) receptor, we applied MM/PBSA to compare the binding modes of caffeine with those of the high-affinity selective antagonist ZM241385.	poly(tetramethylene succinate-co-tetramethylene adipate)	97-101	adenosine A2a receptor	Homo sapiens	57-81
21761181-4	2012	In this study, in order to investigate the interaction of the IGF-II/IGF2R complex and to characterize the binding hot spots of this interaction, a 10 ns molecular dynamics simulation combined with MM-PBSA/MM-GBSA computations and computational alanine scanning was performed on the IGF-II/IGF2R complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	201-205	insulin like growth factor 2	Homo sapiens	62-68
21761181-4	2012	In this study, in order to investigate the interaction of the IGF-II/IGF2R complex and to characterize the binding hot spots of this interaction, a 10 ns molecular dynamics simulation combined with MM-PBSA/MM-GBSA computations and computational alanine scanning was performed on the IGF-II/IGF2R complex.	poly(tetramethylene succinate-co-tetramethylene adipate)	201-205	insulin like growth factor 2 receptor	Homo sapiens	69-74
21559963-0	2012	Binding of BIS like and other ligands with the GSK-3beta kinase: a combined docking and MM-PBSA study.	poly(tetramethylene succinate-co-tetramethylene adipate)	91-95	glycogen synthase kinase 3 beta	Homo sapiens	47-56
21960467-1	2011	We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach.	poly(tetramethylene succinate-co-tetramethylene adipate)	244-248	superoxide dismutase 2	Homo sapiens	90-113
21960467-1	2011	We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach.	poly(tetramethylene succinate-co-tetramethylene adipate)	244-248	superoxide dismutase 2	Homo sapiens	115-120
22087639-6	2012	A sequence of docking to identified transient pockets, starting structure selection based on hot spot information, RMSD clustering and intermolecular docking energies, and MM-PBSA calculations allows one to enrich IL-2 PPIMs from a set of decoys and to discriminate between subgroups of IL-2 PPIMs with low and high affinity.	poly(tetramethylene succinate-co-tetramethylene adipate)	175-179	interleukin 2	Homo sapiens	214-218
23077531-8	2012	Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes.	poly(tetramethylene succinate-co-tetramethylene adipate)	115-119	autoimmune regulator	Homo sapiens	274-283
27468152-7	2011	Additionally molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations for the aliskiren-renin complex provided insight into the binding mode of aliskiren by identifying van der Waals and nonpolar contribution to solvation as the main components of favorable binding interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	68-72	renin	Homo sapiens	117-122
17849398-5	2007	Moreover, in an attempt to add further insight into the ifenprodil mechanism of action, as it is not completely clear if it binds and stabilizes an open or a closed conformation of the NR2B modulatory domain, a matter, which is fundamental for the rational design of NMDA antagonists, MD simulations followed by an MM-PBSA analysis were performed.	poly(tetramethylene succinate-co-tetramethylene adipate)	318-322	glutamate ionotropic receptor NMDA type subunit 2B	Homo sapiens	185-189
21167154-4	2011	The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation.	poly(tetramethylene succinate-co-tetramethylene adipate)	25-29	T cell receptor beta variable 20/OR9-2 (non-functional)	Homo sapiens	124-127
21167154-4	2011	The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation.	poly(tetramethylene succinate-co-tetramethylene adipate)	25-29	T cell receptor beta variable 20/OR9-2 (non-functional)	Homo sapiens	157-160
20469897-3	2010	In this work, the binding affinity and conformational change of the Zif268-DNA complex were successfully reproduced with MD simulations and MM-PBSA analysis.	poly(tetramethylene succinate-co-tetramethylene adipate)	143-147	early growth response 1	Homo sapiens	68-74
20465833-7	2010	In this study, we constructed the first full-atom structural model of Cry4Aa trimer using the trimeric unit cell structure of Cry4Ba toxin as a template and then used the methods of molecular dynamics (MD) and molecular mechanics combined with Poisson-Boltzmann and surface area (MM-PBSA) to show that the trimeric structure of Cry4Aa toxin is stable in 150 mM KCl solution on 10 ns timescale.	poly(tetramethylene succinate-co-tetramethylene adipate)	283-287	cry4AA	Bacillus thuringiensis serovar israelensis	70-76
21822722-0	2011	Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17beta-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps.	poly(tetramethylene succinate-co-tetramethylene adipate)	128-132	hydroxysteroid 17-beta dehydrogenase 1	Homo sapiens	80-91
21167154-4	2011	The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation.	poly(tetramethylene succinate-co-tetramethylene adipate)	25-29	tripartite motif containing 13	Homo sapiens	204-208
20800521-3	2010	To probe the structure of these p22HBP protein complexes, docking, molecular dynamics and MM-PBSA methodologies supported by experimental NMR ring current shift data have been employed.	poly(tetramethylene succinate-co-tetramethylene adipate)	93-97	heme binding protein 1	Mus musculus	32-38
19466465-0	2010	Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA.	poly(tetramethylene succinate-co-tetramethylene adipate)	127-131	cyclin dependent kinase 5	Homo sapiens	29-54
19231824-4	2009	The binding mechanism of HBS helix to Bcl-x(L) and the effect of synthesized cyclic structures are analyzed by MD and MM-PBSA calculations for comparison with the native binding of Bak-Bcl-x(L).	poly(tetramethylene succinate-co-tetramethylene adipate)	121-125	BCL2 like 1	Homo sapiens	38-46
19081253-0	2009	Combining 3D-QSAR, docking, molecular dynamics and MM/PBSA methods to predict binding modes for nonsteroidal selective modulator to glucocorticoid receptor.	poly(tetramethylene succinate-co-tetramethylene adipate)	54-58	nuclear receptor subfamily 3 group C member 1	Homo sapiens	132-155
18186480-5	2008	All these MMP-2 models are subject to 20 ns molecular dynamics (MD) simulations followed by MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	95-99	matrix metallopeptidase 2	Homo sapiens	10-15
17384076-5	2007	The analysis from quantum calculation of binding interaction is consistent with the MM-PBSA calculation of binding free energy, and the calculated free energies for L86/T76-thrombin binding agree well with the experimental data.	poly(tetramethylene succinate-co-tetramethylene adipate)	87-91	coagulation factor II, thrombin	Homo sapiens	173-181
17602517-0	2007	Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.	poly(tetramethylene succinate-co-tetramethylene adipate)	72-76	fatty acid binding protein 2	Rattus norvegicus	47-52
17602517-2	2007	In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details.	poly(tetramethylene succinate-co-tetramethylene adipate)	46-50	fatty acid binding protein 2	Rattus norvegicus	117-154
17602517-2	2007	In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details.	poly(tetramethylene succinate-co-tetramethylene adipate)	46-50	fatty acid binding protein 2	Rattus norvegicus	156-161
16302819-1	2005	The recently described molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for calculating free energies is applied to a congeneric series of 16 ligands to p38 MAP kinase whose binding constants span approximately 2 orders of magnitude.	poly(tetramethylene succinate-co-tetramethylene adipate)	78-82	mitogen-activated protein kinase 14	Homo sapiens	172-175
17181296-4	2006	To understand how PDK1 binds with celecoxib and its derivatives, we have performed extensive molecular docking and combined molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on eight representative PDK1 inhibitors, leading to the finding of a new, more favorable binding mode which is remarkably different from the previously proposed binding mode.	poly(tetramethylene succinate-co-tetramethylene adipate)	219-223	3-phosphoinositide dependent protein kinase 1	Homo sapiens	18-22
34957911-9	2021	MM/PBSA binding free energy analysis revealed that Rhinacanthin Q, subtrifloralacton D, and 7,7""-dimethyllanaraflavone have high binding affinity to HER2.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	erb-b2 receptor tyrosine kinase 2	Homo sapiens	150-154
12471606-4	2003	The relative binding free energies obtained with the MM-PBSA method were 1.5 kcal/mol for 5ADHT, 3.8 kcal/mol for AND, and 4.3 kcal/mol for DHEAS, as compared to TES.	poly(tetramethylene succinate-co-tetramethylene adipate)	56-60	sulfotransferase family 2A member 1	Homo sapiens	140-145
12471606-5	2003	When a water molecule of the ligand binding site, observed in the antibody-TES crystal structure, was explicitly included in MM-PBSA calculations, the relative binding energies were 3.4, 4.9, and 5.4 kcal/mol for 5ADHT, AND, and DHEAS, respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	128-132	sulfotransferase family 2A member 1	Homo sapiens	229-234
12471606-7	2003	The fact that the MM-PBSA method reproduced the relative binding free energies of DHEAS, a steroid having a negatively charged sulfate group, and the neutrally charged TES, 5ADHT, and AND in satisfactory agreement with experiment shows the robustness of the method in predicting relative binding affinities.	poly(tetramethylene succinate-co-tetramethylene adipate)	21-25	sulfotransferase family 2A member 1	Homo sapiens	82-87
33774178-4	2021	In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant.	poly(tetramethylene succinate-co-tetramethylene adipate)	60-64	vitronectin	Homo sapiens	141-150
34289159-9	2021	Further structural behavior of the mutants and native FTO were identified with molecular dynamics simulations and MM-PBSA analyses, along with the 19complex inhibitor compound.	poly(tetramethylene succinate-co-tetramethylene adipate)	117-121	FTO alpha-ketoglutarate dependent dioxygenase	Homo sapiens	54-57
34948899-9	2021	The MM/GBSA binding free energy for Top-1 complex is -28.10 kcal/mol, Top-2 complex is -50.14 kcal/mol) and Control is -46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is -23.38 kcal/mol, -35.29 kcal/mol and -38.20 kcal/mol, respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	144-148	DNA topoisomerase I	Homo sapiens	36-41
34948899-9	2021	The MM/GBSA binding free energy for Top-1 complex is -28.10 kcal/mol, Top-2 complex is -50.14 kcal/mol) and Control is -46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is -23.38 kcal/mol, -35.29 kcal/mol and -38.20 kcal/mol, respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	144-148	DNA topoisomerase I	Homo sapiens	159-164
34690453-12	2021	MM-PBSA provided the basis for analyzing the affinity of the phytochemicals towards Mpro by calculating the binding energy, and secondary structure analysis indicated the stability of protease structure when it is bound to Rutin and Plebeiosides B.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	84-88
34787532-3	2021	The MM-PBSA calculation suggests that TMC-126 loses its potency against mutant variants and PR2 compared to wild-type PR1 mainly due to the loss in intermolecular electrostatic interactions.	poly(tetramethylene succinate-co-tetramethylene adipate)	7-11	transmembrane protein 37	Homo sapiens	118-121
34672012-7	2022	Additionally, it also prioritized Arbutamine-TRR1 as the best drug-target complex based on MM-PBSA (-52.72 kcal/mol), RMSD (2.43 A), and radius of gyration (-21.49 A) analysis.	poly(tetramethylene succinate-co-tetramethylene adipate)	94-98	tRNA-Arg (anticodon TCT) 2-1	Homo sapiens	45-49
34495817-7	2021	Interestingly, molecular dynamics and MM-PBSA results showed that E484K and spike triple mutant complexes were more stable than the N501Y one.	poly(tetramethylene succinate-co-tetramethylene adipate)	41-45	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	76-81
34148296-7	2021	MM-PBSA calculations revealed the stability of hit molecules and PLK-4 complexes in comparison with CFI-400945 and the contribution to binding from key active site residues.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	polo like kinase 4	Homo sapiens	65-70
34581241-3	2021	The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS.	poly(tetramethylene succinate-co-tetramethylene adipate)	128-132	deoxyhypusine synthase	Homo sapiens	235-239
34455930-8	2021	From our dynamic binding free energy calculations using MM/PBSA, asiaticoside, betulinic acid, centellasapogenol, methyl brahmate, and rutin exceeded at least one of the binding energies of the reference compounds, which highlights their strong affinity towards SGLT-2.	poly(tetramethylene succinate-co-tetramethylene adipate)	59-63	solute carrier family 5 member 2	Homo sapiens	262-268
34075338-9	2021	MM-PBSA calculations also revealed the stronger binding of Camostat mesylate to TMPRSS2 active site residues as compared to Nafamostat and BHH.	poly(tetramethylene succinate-co-tetramethylene adipate)	3-7	transmembrane serine protease 2	Homo sapiens	80-87
34492985-5	2021	PLA is mainly subjected to weathering by physical aging; after an initial faster degradation of the amorphous phase, PCL showed a decrease of its degradation rate; similarly to PCL, the degradation of PBSA started from the amorphous phase; PHB is clearly subjected to biological degradation.	poly(tetramethylene succinate-co-tetramethylene adipate)	201-205	PHD finger protein 1	Homo sapiens	177-180
34219624-6	2021	We have computed the binding free energies for the complexes Gal-1-TDG, Gal-1-LBA and Gal-1-G16G using MM/PBSA and are -6.45, -6.22 and -3.08 kcal/mol, respectively.	poly(tetramethylene succinate-co-tetramethylene adipate)	106-110	galectin 1	Homo sapiens	86-91
34903997-7	2021	Our MM-PBSA computation illustrates that ZINC31157475 is more potent (-88.03 kcal mol-1) than nelfinavir (-19.54 kcal mol-1) against COVID-19 3CLp.	poly(tetramethylene succinate-co-tetramethylene adipate)	7-11	calmodulin like 3	Homo sapiens	143-146
35110603-9	2022	Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA.	poly(tetramethylene succinate-co-tetramethylene adipate)	38-42	histone deacetylase 3	Homo sapiens	104-109
35475235-3	2022	Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	182-186	MORN repeat containing 4	Homo sapiens	35-38
35475235-3	2022	Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	182-186	MORN repeat containing 4	Homo sapiens	115-118
35475235-3	2022	Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy.	poly(tetramethylene succinate-co-tetramethylene adipate)	182-186	MORN repeat containing 4	Homo sapiens	154-157
35388744-4	2022	Here, we have chosen a methodology to understand the binding mechanism of these five inhibitors to SARS-CoV-2 Mpro by merging molecular docking, molecular dynamics (MD) simulation and MM-PBSA based free energy calculations.	poly(tetramethylene succinate-co-tetramethylene adipate)	187-191	NEWENTRY	Severe acute respiratory syndrome-related coronavirus	110-114
35273901-7	2022	A systematic computational method combining molecular docking, MM-GBSA binding energy calculation, MD simulations, MM-PBSA binding free energy calculations and ADME were used to find best DPP-4 inhibitor.	poly(tetramethylene succinate-co-tetramethylene adipate)	118-122	dipeptidyl peptidase 4	Homo sapiens	188-193