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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
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Outgoing claims: the papers this work cites, builds on, or argues with.
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A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 2. Case Studies in Molecular Design
inferred← citeshttps://doi.org/10.1021/jm0101141openalex-snapshot
Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides
inferred← citeshttps://doi.org/10.1021/jm0105833openalex-snapshot
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/jm030271vopenalex-snapshot
HierVLS Hierarchical Docking Protocol for Virtual Ligand Screening of Large-Molecule Databases
inferred← citeshttps://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/jm030809xopenalex-snapshot
SYNOPSIS: SYNthesize and OPtimize System in Silico
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/jm0491501openalex-snapshot
AFMoC Enhances Predictivity of 3D QSAR: A Case Study with DOXP-reductoisomerase
inferred← citeshttps://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferred← citeshttps://doi.org/10.1021/jm0498046openalex-snapshot
Native Atom Types for Knowledge-Based Potentials: Application to Binding Energy Prediction
inferred← citeshttps://doi.org/10.1021/jm050043wopenalex-snapshot
M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility
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/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferred← citeshttps://doi.org/10.1021/jm990073xopenalex-snapshot
Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein
inferred← citeshttps://doi.org/10.1021/jp000644topenalex-snapshot
Development of a Knowledge-Based Potential for Crystals of Small Organic Molecules: Calculation of Energy Surfaces for C=0···H−N Hydrogen Bonds
inferred← citeshttps://doi.org/10.1021/jp2010265openalex-snapshot
Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation
inferred← citeshttps://doi.org/10.1023/a:1008005918983openalex-snapshot
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
inferred← citeshttps://doi.org/10.1023/a:1008066310669openalex-snapshot
DREAM++: Flexible docking program for virtual combinatorial libraries
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:1008137707965openalex-snapshot
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
inferred← citeshttps://doi.org/10.1023/a:1008724921888openalex-snapshot
Modifications of the scoring function in FlexX for virtual screening applications
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: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:1011945119287openalex-snapshot
Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches
inferred← citeshttps://doi.org/10.1023/a:1014389729000openalex-snapshot
A genetic algorithm for structure-based de novo design
inferred← citeshttps://doi.org/10.1023/a:1017037831628openalex-snapshot
3D QSAR: current state, scope, and limitations
inferred← citeshttps://doi.org/10.1023/a:1027255820725openalex-snapshot
Binding affinities and non-bonded interaction energies
inferred← citeshttps://doi.org/10.1023/b:jcam.0000030033.26053.40openalex-snapshot
Gaussian mapping of chemical fragments in ligand binding sites
inferred← citeshttps://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferred← citeshttps://doi.org/10.1038/nrd1799openalex-snapshot
Computer-based de novo design of drug-like molecules
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/10.1039/9781788018982-00094openalex-snapshot
Useful Computational Chemistry Tools for Medicinal Chemistry
inferred← citeshttps://doi.org/10.1039/9781847558879-00295openalex-snapshot
Integrated Chemo- and Bioinformatics Approaches to Virtual Screening
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/b509983hopenalex-snapshot
Parallel tempering: Theory, applications, and new perspectives
inferred← citeshttps://doi.org/10.1039/b608269fopenalex-snapshot
Molecular mechanics methods for predicting protein–ligand binding
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/10.1055/s-0040-1719873openalex-snapshot
Synthesis of Novel Pyrazine-Substituted 1H-Pyrrole-2-carboxamides and Related Tethered Heterocycles
inferred← citeshttps://doi.org/10.1063/1.4818908openalex-snapshot
Perspective: Coarse-grained models for biomolecular systems
inferred← citeshttps://doi.org/10.1071/ch04161openalex-snapshot
The Role of Virtual Screening in Computer Aided Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1073/pnas.032673399openalex-snapshot
Combinatorial computational method gives new picomolar ligands for a known enzyme
inferred← citeshttps://doi.org/10.1073/pnas.1006428107openalex-snapshot
Recovering physical potentials from a model protein databank
inferred← citeshttps://doi.org/10.1073/pnas.96.18.9997openalex-snapshot
The maximal affinity of ligands
inferred← citeshttps://doi.org/10.1074/jbc.m204514200openalex-snapshot
CH···O Hydrogen Bonds at Protein-Protein Interfaces
inferred← citeshttps://doi.org/10.1080/15376516.2017.1351506openalex-snapshot
A significant mechanism of molecular recognition between bioflavonoids and P-glycoprotein leading to herb-drug interactions
inferred← citeshttps://doi.org/10.1088/2632-2153/ace58copenalex-snapshot
Semi-equivariant conditional normalizing flows, with applications to target-aware molecule generation
inferred← citeshttps://doi.org/10.1093/bib/bbac603openalex-snapshot
Leveraging scaffold information to predict protein–ligand binding affinity with an empirical graph neural network
inferred← citeshttps://doi.org/10.1093/bib/bbv037openalex-snapshot
Building a virtual ligand screening pipeline using free software: a survey
inferred← citeshttps://doi.org/10.1093/nar/gki204openalex-snapshot
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
inferred← citeshttps://doi.org/10.1110/ps.9.4.765openalex-snapshot
Analysis of knowledge‐based protein‐ligand potentials using a self‐consistent method
inferred← citeshttps://doi.org/10.1111/j.1582-4934.2008.00665.xopenalex-snapshot
Docking, virtual high throughput screening and in silico fragment‐based drug design
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