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VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Shape Complementarity at Protein/Protein Interfaces
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A Continuum Model for Protein–Protein Interactions: Application to the Docking Problem
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Synthesis of high specific activity (+)- and (-)-6-[18F]fluoronorepinephrine via the nucleophilic aromatic substitution reaction
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De novo design of ligands /spl lsqb/automated drug design/spl rsqb/
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data
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PBSA_E: A PBSA-Based Free Energy Estimator for Protein–Ligand Binding Affinity
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Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein−Ligand Complexes
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CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci200193zopenalex-snapshot
AADS- An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
inferred← citeshttps://doi.org/10.1021/ci200306wopenalex-snapshot
Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-BasedDe NovoDesign: Study of Binding Mode of Diastereomer Compounds
inferred← citeshttps://doi.org/10.1021/ci300493wopenalex-snapshot
ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci400321ropenalex-snapshot
Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein–Ligand Complexes Using Support Vector Machines
inferred← citeshttps://doi.org/10.1021/ci9002987openalex-snapshot
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci9004139openalex-snapshot
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
inferred← citeshttps://doi.org/10.1021/ic0202920openalex-snapshot
HostDesigner: A Program for the de Novo Structure-Based Design of Molecular Receptors with Binding Sites that Complement Metal Ion Guests
inferred← citeshttps://doi.org/10.1021/jm000467kopenalex-snapshot
Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
inferred← citeshttps://doi.org/10.1021/jm010904aopenalex-snapshot
Synthesis, Biological Evaluation, and Binding Mode of Novel 1-[2-(Diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles Targeted at the HIV-1 Reverse Transcriptase
inferred← citeshttps://doi.org/10.1021/jm011088+openalex-snapshot
Binding Mode Analysis of 3-(4-Benzoyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide: A New Synthetic Histone Deacetylase Inhibitor Inducing Histone Hyperacetylation, Growth Inhibition, and Terminal Cell Differentiation
inferred← citeshttps://doi.org/10.1021/jm015515vopenalex-snapshot
3-(4-Aroyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides, a New Class of Synthetic Histone Deacetylase Inhibitors
inferred← citeshttps://doi.org/10.1021/jm0200299openalex-snapshot
Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water
inferred← citeshttps://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferred← citeshttps://doi.org/10.1021/jm048973nopenalex-snapshot
Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein−Ligand Complexes
inferred← citeshttps://doi.org/10.1021/jm049050vopenalex-snapshot
A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands
inferred← citeshttps://doi.org/10.1021/jm049444mopenalex-snapshot
Quantitative Structure−Activity Relationship (5D-QSAR) Study of Combretastatin-like Analogues as Inhibitors of Tubulin Assembly
inferred← citeshttps://doi.org/10.1021/jm050260xopenalex-snapshot
Development of Quantitative Structure−Binding Affinity Relationship Models Based on Novel Geometrical Chemical Descriptors of the Protein−Ligand Interfaces
inferred← citeshttps://doi.org/10.1021/jm500284xopenalex-snapshot
Exploring the Role of 2-Chloro-6-fluoro Substitution in 2-Alkylthio-6-benzyl-5-alkylpyrimidin-4(3H)-ones: Effects in HIV-1-Infected Cells and in HIV-1 Reverse Transcriptase Enzymes
inferred← citeshttps://doi.org/10.1021/jm970273dopenalex-snapshot
A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis
inferred← citeshttps://doi.org/10.1021/jm9910775openalex-snapshot
Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins
inferred← citeshttps://doi.org/10.1021/jp0044476openalex-snapshot
Binding Affinities for a Series of Selective Inhibitors of Gelatinase-A Using Molecular Dynamics with a Linear Interaction Energy Approach
inferred← citeshttps://doi.org/10.1023/a:1007929626986openalex-snapshot
Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
inferred← citeshttps://doi.org/10.1023/a:1007930623000openalex-snapshot
Ligand binding affinity prediction by linear interaction energy methods
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1023/a:1007999920146openalex-snapshot
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
inferred← citeshttps://doi.org/10.1023/a:1008040323669openalex-snapshot
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
inferred← citeshttps://doi.org/10.1023/a:1008073215919openalex-snapshot
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
inferred← citeshttps://doi.org/10.1023/a:1008094712424openalex-snapshot
PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
inferred← citeshttps://doi.org/10.1023/a:1008137707965openalex-snapshot
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
inferred← citeshttps://doi.org/10.1023/a:1008729005958openalex-snapshot
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
inferred← citeshttps://doi.org/10.1023/a:1008737207775openalex-snapshot
Virtual screening with solvation and ligand-induced complementarity
inferred← citeshttps://doi.org/10.1023/a:1008781006867openalex-snapshot
Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
inferred← citeshttps://doi.org/10.1023/a:1011188704521openalex-snapshot
Protein ligand docking based on empirical method for binding affinity estimation
inferred← citeshttps://doi.org/10.1023/a:1011903711265openalex-snapshot
Recent advances in structure-based ligand design using molecular dynamics and Monte Carlo methods.
inferred← citeshttps://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferred← citeshttps://doi.org/10.1023/a:1017037831628openalex-snapshot
3D QSAR: current state, scope, and limitations
inferred← citeshttps://doi.org/10.1023/a:1017057332537openalex-snapshot
Recent progress in CoMFA methodology and related techniques
inferred← citeshttps://doi.org/10.1023/a:1022446720849openalex-snapshot
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
inferred← citeshttps://doi.org/10.1023/a:1027207904795openalex-snapshot
Molecular mechanics calculations on protein-ligand complexes
inferred← citeshttps://doi.org/10.1023/a:1027247618908openalex-snapshot
Comparative binding energy analysis
inferred← citeshttps://doi.org/10.1023/a:1027251719816openalex-snapshot
A priori prediction of ligand affinity by energy minimization
inferred← citeshttps://doi.org/10.1023/a:1027255820725openalex-snapshot
Binding affinities and non-bonded interaction energies
inferred← citeshttps://doi.org/10.1023/a:1027299602978openalex-snapshot
Receptor-based prediction of binding affinities
inferred← citeshttps://doi.org/10.1023/b:jcam.0000005748.19093.e8openalex-snapshot
Inhibition and substrate recognition – a computational approach applied to HIV protease
inferred← citeshttps://doi.org/10.1023/b:jcam.0000017362.66268.d5openalex-snapshot
Development and testing of a de novo drug-design algorithm
inferred← citeshttps://doi.org/10.1023/b:jcam.0000021882.99270.4copenalex-snapshot
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
inferred← citeshttps://doi.org/10.1038/nsmb.2305openalex-snapshot
Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element
inferred← citeshttps://doi.org/10.1038/sj.bjp.0707515openalex-snapshot
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
inferred← citeshttps://doi.org/10.1039/9781788010139-00001openalex-snapshot
Computational Chemistry and Molecular Modelling Basics
inferred← citeshttps://doi.org/10.1039/9781847550705-00001openalex-snapshot
Molecular informatics: Sharpening drug design's cutting edge
inferred← citeshttps://doi.org/10.1039/9781847558879-00295openalex-snapshot
Integrated Chemo- and Bioinformatics Approaches to Virtual Screening
inferred← citeshttps://doi.org/10.1039/9781849735377-00080openalex-snapshot
Continuum Solvation in Biomolecular Systems
inferred← citeshttps://doi.org/10.1039/b402399dopenalex-snapshot
Theoretical analysis of peptidyl α-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design
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/c0md00165aopenalex-snapshot
Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets
inferred← citeshttps://doi.org/10.1063/5.0287651openalex-snapshot
In silico drug design and analysis of HGPRT inhibitor against malaria
inferred← citeshttps://doi.org/10.1073/pnas.032673399openalex-snapshot
Combinatorial computational method gives new picomolar ligands for a known enzyme
inferred← citeshttps://doi.org/10.1074/mcp.m200054-mcp200openalex-snapshot
A New Method to Estimate Ligand-Receptor Energetics
inferred← citeshttps://doi.org/10.1080/08927020802430752openalex-snapshot
Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)
inferred← citeshttps://doi.org/10.1080/10629360108035372openalex-snapshot
MTD-PLS: A PLS-Based Variant of the MTD Method. A 3D-QSAR Analysis of Receptor Affinities for a Series of Halogenated Dibenzoxin and Biphenyl Derivatives
inferred← citeshttps://doi.org/10.1093/bib/bbp023openalex-snapshot
Recent advances in computer-aided drug design
inferred← citeshttps://doi.org/10.1093/chromsci/bmab140openalex-snapshot
Online Solid-Phase Extraction of Prometon and Prometryne Using MIL-101(Cr) as Sorbent before Gas Chromatographic Analysis: A Computational and Experimental Study and Comparison between Splitless and PTV Inlets
inferred← citeshttps://doi.org/10.1093/nar/gkj039openalex-snapshot
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
inferred← citeshttps://doi.org/10.1093/protein/12.6.469openalex-snapshot
Molecular mechanics analysis of drug-resistant mutants of HIV protease
inferred← citeshttps://doi.org/10.1101/2024.12.02.626325openalex-snapshot
DoRIAT: A Bayesian framework for interpreting and annotating docking runs
inferred← citeshttps://doi.org/10.1101/2025.08.17.670706openalex-snapshot
AMODO-EO: A Practical Framework for Adaptive Objective Discovery in Multi-Objective Drug Optimization
inferred← citeshttps://doi.org/10.1109/cibcb.2008.4675787openalex-snapshot
Using hybrid GA-ANN to predict biological activity of HIV protease inhibitors
inferred← citeshttps://doi.org/10.1110/ps.8.5.1134openalex-snapshot
The effect of multiple binding modes on empirical modeling of ligand docking to proteins
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