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Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase

https://doi.org/10.1021/jm050306m
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Outgoing claims: the papers this work cites, builds on, or argues with.

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CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
inferred← citeshttps://doi.org/10.1021/ci4001794openalex-snapshot
Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations
inferred← citeshttps://doi.org/10.1021/ci5003203openalex-snapshot
Evaluation and Application of MD-PB/SA in Structure-Based Hierarchical Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci600412zopenalex-snapshot
Comparative Evaluation of MMPBSA and XSCORE To Compute Binding Free Energy in XIAP−Peptide Complexes
inferred← citeshttps://doi.org/10.1021/ci700041jopenalex-snapshot
Rapid Estimation of Relative Protein−Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA
inferred← citeshttps://doi.org/10.1021/ci700470copenalex-snapshot
Investigation of MM-PBSA Rescoring of Docking Poses
inferred← citeshttps://doi.org/10.1021/ci800313hopenalex-snapshot
Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case
inferred← citeshttps://doi.org/10.1021/ci9004628openalex-snapshot
Assessment of a Novel Scoring Method Based on Solvent Accessible Surface Area Descriptors
inferred← citeshttps://doi.org/10.1021/ci900497dopenalex-snapshot
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
inferred← citeshttps://doi.org/10.1021/ci9005047openalex-snapshot
A Computational Approach to the Study of the Binding Mode of Dual ACE/NEP Inhibitors
inferred← citeshttps://doi.org/10.1021/ct100245nopenalex-snapshot
Modeling Protein−Ligand Binding by Mining Minima
inferred← citeshttps://doi.org/10.1021/ct100504hopenalex-snapshot
Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/ct200244popenalex-snapshot
A Direct Comparison of the MM-GB/SA Scoring Procedure and Free-Energy Perturbation Calculations Using Carbonic Anhydrase as a Test Case: Strengths and Pitfalls of Each Approach
inferred← citeshttps://doi.org/10.1021/ct3001377openalex-snapshot
Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors
inferred← citeshttps://doi.org/10.1021/ct300899nopenalex-snapshot
Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore
inferred← citeshttps://doi.org/10.1021/ct4007037openalex-snapshot
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
inferred← citeshttps://doi.org/10.1021/ct400914wopenalex-snapshot
Role of Deprotonation Free Energies in p K a Prediction and Molecule Ranking
inferred← citeshttps://doi.org/10.1021/ja0779250openalex-snapshot
Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases
inferred← citeshttps://doi.org/10.1021/jm060522aopenalex-snapshot
Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
inferred← citeshttps://doi.org/10.1021/jm0608210openalex-snapshot
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
inferred← citeshttps://doi.org/10.1021/jm060999mopenalex-snapshot
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
inferred← citeshttps://doi.org/10.1021/jm061021sopenalex-snapshot
Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization?
inferred← citeshttps://doi.org/10.1021/jm800524sopenalex-snapshot
Hit Identification and Binding Mode Predictions by Rigorous Free Energy Simulations
inferred← citeshttps://doi.org/10.1021/jm801399ropenalex-snapshot
Novel Lead Structures for p38 MAP Kinase via FieldScreen Virtual Screening
inferred← citeshttps://doi.org/10.1021/jp0713763openalex-snapshot
Molecular Insight into the Interaction between IFABP and PA by Using MM−PBSA and Alanine Scanning Methods
inferred← citeshttps://doi.org/10.1021/jp104983aopenalex-snapshot
Structural and Thermodynamic Characteristics of the Exosite Binding Pocket on the Human BACE1: A Molecular Modeling Approach
inferred← citeshttps://doi.org/10.1021/jp2022049openalex-snapshot
Computational Study of the Binding Modes of Caffeine to the Adenosine A2AReceptor
inferred← citeshttps://doi.org/10.1021/jp304304vopenalex-snapshot
Understanding the Interaction between Valsartan and Detergents by NMR Techniques and Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1021/jp411111gopenalex-snapshot
Molecular Dynamics Simulation Studies on the Positive Cooperativity of the Kemptide Substrate with Protein Kinase A Induced by the ATP Ligand
inferred← citeshttps://doi.org/10.1021/jp802648kopenalex-snapshot
QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins
inferred← citeshttps://doi.org/10.1021/jp9059664openalex-snapshot
Explicitly Solvated Ligand Contribution to Continuum Solvation Models for Binding Free Energies: Selectivity of Theophylline Binding to an RNA Aptamer
inferred← citeshttps://doi.org/10.1021/jp911689ropenalex-snapshot
Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors
inferred← citeshttps://doi.org/10.1021/mp900131popenalex-snapshot
Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation
inferred← citeshttps://doi.org/10.1038/s41598-021-91196-1openalex-snapshot
A novel piperazine derivative that targets hepatitis B surface antigen effectively inhibits tenofovir resistant hepatitis B virus
inferred← citeshttps://doi.org/10.1039/9781849735377-00195openalex-snapshot
Binding Free Energy Calculation and Scoring in Small-Molecule Docking
inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferred← citeshttps://doi.org/10.1039/c2mb25217aopenalex-snapshot
Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity
inferred← citeshttps://doi.org/10.1039/c2sc00895eopenalex-snapshot
Mutational Locally Enhanced Sampling (MULES) for quantitative prediction of the effects of mutations at protein–protein interfaces
inferred← citeshttps://doi.org/10.1039/c3cp53537aopenalex-snapshot
A conformational factorisation approach for estimating the binding free energies of macromolecules
inferred← citeshttps://doi.org/10.1039/c5cp06024aopenalex-snapshot
Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme
inferred← citeshttps://doi.org/10.1039/c8cp01886copenalex-snapshot
In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment
inferred← citeshttps://doi.org/10.1039/d2cp04584bopenalex-snapshot
Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics
inferred← citeshttps://doi.org/10.1039/d5ra05535kopenalex-snapshot
Multi-omics pan-cancer profiling of CDK2 and in silico identification of plant-derived inhibitors using machine learning approaches
inferred← citeshttps://doi.org/10.1063/1.2904461openalex-snapshot
Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling
inferred← citeshttps://doi.org/10.1063/1.3119261openalex-snapshot
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations
inferred← citeshttps://doi.org/10.1063/1.4733951openalex-snapshot
Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril
inferred← citeshttps://doi.org/10.1063/1.4769292openalex-snapshot
Perspective: Alchemical free energy calculations for drug discovery
inferred← citeshttps://doi.org/10.1074/jbc.m110.109660openalex-snapshot
Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
inferred← citeshttps://doi.org/10.1080/07391102.2023.2294376openalex-snapshot
Novel computational and drug design strategies for the inhibition of human T-cell leukemia virus 1-associated lymphoma by Astilbin derivatives
inferred← citeshttps://doi.org/10.1080/08927021003628871openalex-snapshot
A computational analysis of pyrazole-based inhibitors binding to Hsp90 using molecular dynamics simulation and the MM-GBSA method
inferred← citeshttps://doi.org/10.1080/10610270802613562openalex-snapshot
Free energy perturbation and MM/PBSA studies on inclusion complexes of some structurally related compounds with β-cyclodextrin
inferred← citeshttps://doi.org/10.1080/21553769.2013.815137openalex-snapshot
Design of potent inhibitors of acetylcholinesterase using morin as the starting compound
inferred← citeshttps://doi.org/10.1093/bib/bbaa107openalex-snapshot
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
inferred← citeshttps://doi.org/10.1107/s090744491201997xopenalex-snapshot
X-ray structure of p38α bound to TAK-715: comparison with three classic inhibitors
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2007.00571.xopenalex-snapshot
Signposts of Docking and Scoring in Drug Design
inferred← citeshttps://doi.org/10.1142/9789812778789_0019openalex-snapshot
Molecular Dynamics-based Free Energy Simulations
inferred← citeshttps://doi.org/10.1142/9789812838780_0010openalex-snapshot
Molecular Modeling of Proteins: From Simulations to Drug Design Applications
inferred← citeshttps://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1186/2046-1682-7-5openalex-snapshot
Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking
inferred← citeshttps://doi.org/10.1273/cbij.10.32openalex-snapshot
Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches
inferred← citeshttps://doi.org/10.13040/ijpsr.0975-8232.12(6).3104-19openalex-snapshot
inferred← citeshttps://doi.org/10.1371/journal.pone.0135421openalex-snapshot
The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study
inferred← citeshttps://doi.org/10.1371/journal.pone.0337970openalex-snapshot
Exploring potential phytocompounds from black cumin as drug molecules against SARS-CoV-2 infections through bioinformatics analysis
inferred← citeshttps://doi.org/10.1515/psr-2020-0034openalex-snapshot
Computational methods for calculation of protein-ligand binding affinities in structure-based drug design
inferred← citeshttps://doi.org/10.1517/17460441.1.4.335openalex-snapshot
Incorporating protein flexibility into docking and structure-based drug design
inferred← citeshttps://doi.org/10.1517/17460441.2.4.469openalex-snapshot
Ligand efficiency indices for effective drug discovery
inferred← citeshttps://doi.org/10.1517/17460441.2015.1032936openalex-snapshot
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
inferred← citeshttps://doi.org/10.1529/biophysj.106.082941openalex-snapshot
Ensemble-Based Convergence Analysis of Biomolecular Trajectories
inferred← citeshttps://doi.org/10.1529/biophysj.106.099150openalex-snapshot
Quantum and Molecular Dynamics Study for Binding of Macrocyclic Inhibitors to Human α-Thrombin
inferred← citeshttps://doi.org/10.17192/z2006.0842openalex-snapshot
Characterization of Binding Pocket Flexibility of Aldose Reductase
inferred← citeshttps://doi.org/10.18231/j.jpbs.2021.008openalex-snapshot
Molecular docking studies of 1,3,4 -thiadiazoles as myeloperoxidase inhibitors
inferred← citeshttps://doi.org/10.2174/1570180819666220530152026openalex-snapshot
Identification of Novel Nontoxic Mutants of Diphtheria Toxin Unable to ADP-ribosylate EF2 Using Molecular Dynamics Simulations and Free Energy Calculations
inferred← citeshttps://doi.org/10.25560/17988openalex-snapshot
Predicting structural and energetic effects of mutations at protein-protein interfaces
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-dh114openalex-snapshot
Accurate prediction of ligand binding for a flexible protein using P-score ranking.
inferred← citeshttps://doi.org/10.3329/bjp.v8i3.15110openalex-snapshot
In silico docking studies of RP2 (X-Linked retinitis pigmentosa) protein using anthocyanins as potential inhibitors
inferred← citeshttps://doi.org/10.3390/biom11081104openalex-snapshot
Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics Approaches
inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/ijms17060819openalex-snapshot
Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor
inferred← citeshttps://doi.org/10.3390/molecules28062767openalex-snapshot
Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation
inferred← citeshttps://doi.org/10.4018/978-1-60960-860-6.ch015openalex-snapshot
Computational Techniques in Binding Affinity Prediction of Drugs
inferred← citeshttps://doi.org/10.5772/37107openalex-snapshot
MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies
inferred← citeshttps://doi.org/10.58837/chula.the.2020.94openalex-snapshot
Effect of pyridoxal phosphate and tetrahydrofolate bound on human serine hydroxymethyltransferase by molecular dynamic simulation
inferred← citeshttps://doi.org/10.70675/48e8ac59z3fecz4841za036z40e6a446b0ccopenalex-snapshot
Modeling and Standard Binding Free Energy Calculations of Complex Biological Objects
inferred← citeshttps://doi.org/10.70675/6f0af6e8z43cdz4f3czb462z86c0726d15b4openalex-snapshot
Bases moléculaire de l'interaction protéine-protéine lors de la synaptogenèse
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