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DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
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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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Evaluation of the CASP2 docking section
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Interactions with Aromatic Rings in Chemical and Biological Recognition
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Fluorine Interactions at the Thrombin Active Site: Protein Backbone Fragments HCαCO Comprise a Favorable CF Environment and Interactions of CF with Electrophiles
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Specific empirical free energy function for automated docking of carbohydrates to proteins
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Molecular similarity based on electrostatic potential and electric field
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The Use of Composite Crystal-field Environments in Molecular Recognition and the de Novo Design of Protein Ligands
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SuperStar: A Knowledge-based Approach for Identifying Interaction Sites in Proteins
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Knowledge-based scoring function to predict protein-ligand interactions
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Superstar: comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions 1 1Edited by R. Huber
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The Hydrophobic Effect: Formation of Micelles and Biological Membranes
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Knowledge-based potentials for proteins
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Chris Lipinski discusses life and chemistry after the Rule of Five
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Predicting Protein−Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine-Learning Methods
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Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors
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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes
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Novel Scoring Functions Comprising QXP, SASA, and Protein Side-Chain Entropy Terms
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Evaluation of Docking Functions for Protein−Ligand Docking
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SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
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A novel scoring function for molecular docking
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Design, synthesis and biological evaluation of Pontin ATPase inhibitors through a molecular docking approach
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Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities
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Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank
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Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches
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Structure-based grafting and identification of kinase–inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma
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Drug-target interaction/affinity prediction: Deep learning models and advances review
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A new reactive potential for the molecular dynamics simulation of liquid water
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Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death
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Virtual ligand screening: strategies, perspectives and limitations
inferred← citeshttps://doi.org/10.1016/j.drudis.2007.12.002openalex-snapshot
Towards improving compound selection in structure-based virtual screening
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Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts
inferred← citeshttps://doi.org/10.1016/j.drudis.2021.09.007openalex-snapshot
Machine-learning methods for ligand–protein molecular docking
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An in vitro and in vivo evaluation of new potential trans -sialidase inhibitors of Trypanosoma cruzi predicted by a computational drug repositioning method
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Direct modification of the 5-HT3 receptor current by some anticancer drugs
inferred← citeshttps://doi.org/10.1016/j.future.2025.107863openalex-snapshot
Harnessing quality-throughput trade-off in scoring functions for extreme-scale virtual screening campaigns
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An electronic environment and contact direction sensitive scoring function for predicting affinities of protein–ligand complexes in Contour®
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Scaffold-based analysis of nonpeptide oncogenic FTase inhibitors using multiple similarity matching, binding affinity scoring and enzyme inhibition assay
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RLBindDeep: A ResNet-LSTM based novel framework for protein–ligand binding affinity prediction
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Structural bioinformatics for rational drug design
inferred← citeshttps://doi.org/10.1016/j.str.2011.07.019openalex-snapshot
Structure of the Yersinia pestis FabV Enoyl-ACP Reductase and Its Interaction with Two 2-Pyridone Inhibitors
inferred← citeshttps://doi.org/10.1016/j.str.2023.02.010openalex-snapshot
Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation
inferred← citeshttps://doi.org/10.1016/j.ymeth.2017.08.010openalex-snapshot
Function and structure-based screening of compounds, peptides and proteins to identify drug candidates
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot
Mean-Force Scoring Functions for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1017/cbo9781139021500.024openalex-snapshot
Basic Principles and Practices of Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot
Protein flexibility in docking and surface mapping
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00474openalex-snapshot
Development of a New Scoring Function for Virtual Screening: APBScore
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00542openalex-snapshot
Guiding Conventional Protein–Ligand Docking Software with Convolutional Neural Networks
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00263openalex-snapshot
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01537openalex-snapshot
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00127openalex-snapshot
Predicting Protein–Ligand Docking Structure with Graph Neural Network
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01149openalex-snapshot
Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c02054openalex-snapshot
Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01014openalex-snapshot
Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00709openalex-snapshot
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00201openalex-snapshot
Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00427openalex-snapshot
Improved Prediction of Drug–Protein Interactions through Physics-Based Few-Shot Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00373openalex-snapshot
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00111openalex-snapshot
CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c02173openalex-snapshot
DESPOT: Direction-Enhanced Scoring POTentials for Scoring of Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00226openalex-snapshot
Rigidity Strengthening: A Mechanism for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00545openalex-snapshot
Comparative Assessment of Scoring Functions: The CASF-2016 Update
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00582openalex-snapshot
Converging a Knowledge-Based Scoring Function: DrugScore2018
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00334openalex-snapshot
AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00356openalex-snapshot
Random Forest Refinement of Pairwise Potentials for Protein–Ligand Decoy Detection
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c01184openalex-snapshot
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00503openalex-snapshot
FFENCODER-PL: Pair Wise Energy Descriptors for Protein-Ligand Pose Selection
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01691openalex-snapshot
CHARMM-GUI EnzyDocker for Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00516openalex-snapshot
Generation of Pairwise Potentials Using Multidimensional Data Mining
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00366openalex-snapshot
EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.6b00479openalex-snapshot
Oxime Ethers of (E)-11-Isonitrosostrychnine as Highly Potent Glycine Receptor Antagonists
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04421openalex-snapshot
Iterative Knowledge-Based Scoring Function for Protein–Ligand Interactions by Considering Binding Affinity Information
inferred← citeshttps://doi.org/10.1021/acsomega.1c04996openalex-snapshot
Prediction of Binding Free Energy of Protein–Ligand Complexes with a Hybrid Molecular Mechanics/Generalized Born Surface Area and Machine Learning Method
inferred← citeshttps://doi.org/10.1021/acsomega.7b01194openalex-snapshot
A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions
inferred← citeshttps://doi.org/10.1021/bi5014358openalex-snapshot
An Ordered Water Channel in Staphylococcus aureus FabI: Unraveling the Mechanism of Substrate Recognition and Reduction
inferred← citeshttps://doi.org/10.1021/bi702156hopenalex-snapshot
Probing the Acyl-Binding Pocket of Aminoacylase-1
inferred← citeshttps://doi.org/10.1021/ci100036aopenalex-snapshot
Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci100214aopenalex-snapshot
Rapid Context-Dependent Ligand Desolvation in Molecular Docking
inferred← citeshttps://doi.org/10.1021/ci100250zopenalex-snapshot
Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods
inferred← citeshttps://doi.org/10.1021/ci1003009openalex-snapshot
Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy
inferred← citeshttps://doi.org/10.1021/ci100343jopenalex-snapshot
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
inferred← citeshttps://doi.org/10.1021/ci100368topenalex-snapshot
Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies
inferred← citeshttps://doi.org/10.1021/ci100473dopenalex-snapshot
Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors
inferred← citeshttps://doi.org/10.1021/ci2000665openalex-snapshot
Ligand Identification Scoring Algorithm (LISA)
inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/ci200082topenalex-snapshot
CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci200098vopenalex-snapshot
MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions
inferred← citeshttps://doi.org/10.1021/ci200220vopenalex-snapshot
Robust Scoring Functions for Protein–Ligand Interactions with Quantum Chemical Charge Models
inferred← citeshttps://doi.org/10.1021/ci200274qopenalex-snapshot
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci200377uopenalex-snapshot
Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci2003939openalex-snapshot
Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
inferred← citeshttps://doi.org/10.1021/ci300619xopenalex-snapshot
Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci400045vopenalex-snapshot
Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark
inferred← citeshttps://doi.org/10.1021/ci400302dopenalex-snapshot
HotLig: A Molecular Surface-Directed Approach to Scoring Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci400450hopenalex-snapshot
Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor
inferred← citeshttps://doi.org/10.1021/ci500081mopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
inferred← citeshttps://doi.org/10.1021/ci500156dopenalex-snapshot
Kernel Density Estimation Applied to Bond Length, Bond Angle, and Torsion Angle Distributions
inferred← citeshttps://doi.org/10.1021/ci5002026openalex-snapshot
Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2
inferred← citeshttps://doi.org/10.1021/ci5003735openalex-snapshot
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA
inferred← citeshttps://doi.org/10.1021/ci500731aopenalex-snapshot
Classification of Current Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci700134popenalex-snapshot
DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci7004669openalex-snapshot
AIScore — Chemically Diverse Empirical Scoring Function Employing Quantum Chemical Binding Energies of Hydrogen-Bonded Complexes
inferred← citeshttps://doi.org/10.1021/ci700470copenalex-snapshot
Investigation of MM-PBSA Rescoring of Docking Poses
inferred← citeshttps://doi.org/10.1021/ci7004719openalex-snapshot
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
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