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Critical evaluation of methods to incorporate entropy loss upon binding in high‐throughput docking

https://doi.org/10.1002/prot.21180
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Flexible docking using tabu search and an empirical estimate of binding affinity
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ChemInform Abstract: A PROTON NMR STUDY OF THE INTERACTIONS AND CONFORMATIONS OF RATIONALLY DESIGNED BRODIMOPRIM ANALOGS IN COMPLEXES WITH LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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Flexible ligand docking using conformational ensembles
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Pharmacophore‐based molecular docking to account for ligand flexibility
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Automated docking of substrates to proteins by simulated annealing
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Knowledge-based scoring function to predict protein-ligand interactions
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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Inhibition of dihydrofolate reductase from bacterial and vertebrate sources by folate, aminopterin, methotrexate and their 5-deaza analogues
inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
inferredcites →https://doi.org/10.1016/s0006-3495(04)74084-9openalex-snapshot
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
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The statistical-thermodynamic basis for computation of binding affinities: a critical review
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Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
inferredcites →https://doi.org/10.1016/s0039-128x(01)00194-5openalex-snapshot
The ligand binding profiles of estrogen receptors α and β are species dependent
inferredcites →https://doi.org/10.1016/s1359-6446(97)01163-xopenalex-snapshot
Virtual screening—an overview
inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot
High-throughput docking for lead generation
inferredcites →https://doi.org/10.1021/bi00009a018openalex-snapshot
Role of the Active-Site Carboxylate in Dihydrofolate Reductase: Kinetic and Spectroscopic Studies of the Aspartate 26 .fwdarw. Asparagine Mutant of the Lactobacillus casei Enzyme
inferredcites →https://doi.org/10.1021/bi00528a021openalex-snapshot
Negative cooperativity between folinic acid and coenzyme in their binding to L. casei dihydrofolate reductase
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
inferredcites →https://doi.org/10.1021/ja01973a015openalex-snapshot
THE MICROSCOPY OF VEGETABLE FOODS WITH SPECIAL REFERENCE TO THE DETECTION OF ADULTERATION AND THE DIAGNOSIS OF MIXTURES.
inferredcites →https://doi.org/10.1021/ja038496iopenalex-snapshot
A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/jm00026a001openalex-snapshot
Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
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Synthesis of the antileukemic agents 5,10-dideazaaminopterin and 5,10-dideaza-5,6,7,8-tetrahydroaminopterin
inferredcites →https://doi.org/10.1021/jm00378a025openalex-snapshot
A proton NMR study of the interactions and conformations of rationally designed brodimoprim analogs in complexes with Lactobacillus casei dihydrofolate reductase
inferredcites →https://doi.org/10.1021/jm010548wopenalex-snapshot
Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B
inferredcites →https://doi.org/10.1021/jm0300173openalex-snapshot
Nuclear Hormone Receptor Targeted Virtual Screening
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm950786popenalex-snapshot
2,4-Diamino-5-deaza-6-Substituted Pyrido[2,3-d]pyrimidine Antifolates as Potent and Selective Nonclassical Inhibitors of Dihydrofolate Reductases
inferredcites →https://doi.org/10.1021/jm980081yopenalex-snapshot
Structure-Based Design and Synthesis of Lipophilic 2,4-Diamino-6-Substituted Quinazolines and Their Evaluation as Inhibitors of Dihydrofolate Reductases and Potential Antitumor Agents
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jm990408aopenalex-snapshot
Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1008121029716openalex-snapshot
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1023/a:1015930826903openalex-snapshot
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
inferredcites →https://doi.org/10.1073/pnas.162365999openalex-snapshot
On the calculation of absolute macromolecular binding free energies
inferredcites →https://doi.org/10.1073/pnas.68.8.1678openalex-snapshot
Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect
inferredcites →https://doi.org/10.1073/pnas.97.3.1008openalex-snapshot
Rational discovery of novel nuclear hormone receptor antagonists
inferredcites →https://doi.org/10.1093/emboj/18.17.4608openalex-snapshot
Structure of the ligand‐binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1159/000238239openalex-snapshot
Properties of Brodimoprim as an Inhibitor of Dihydrofolate Reductases

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Recent Trends in Structure‐Based Drug Design and Energetics
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Protein Flexibility in In Silico Screening
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(Thermo)dynamic Role of Receptor Flexibility, Entropy, and Motional Correlation in Protein–Ligand Binding
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LigDockCSA: Protein–ligand docking using conformational space annealing
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A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
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Application of NMR and Molecular Docking in Structure-Based Drug Discovery
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Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
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PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements
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MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization
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Theory of Free Energy and Entropy in Noncovalent Binding
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Protein–Ligand Binding Free Energies from Exhaustive Docking
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Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
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