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Flexible ligand docking using a genetic algorithm
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Flexible docking of ligands to receptor sites using genetic algorithms
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Role of structure-based drug design (SBDD) in the repurposing and discovery of anti-viral leads against Monkeypox virus disease
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Combining a genetic algorithm with a linear scaling semiempirical method for protein–ligand docking
inferred← citeshttps://doi.org/10.1016/s0006-291x(03)01000-3openalex-snapshot
Establishment and functional validation of a structural homology model for human DNA methyltransferase 1
inferred← citeshttps://doi.org/10.1016/s0006-3495(03)75033-4openalex-snapshot
Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities
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Protein-protein recognition
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Computational tools for structure-based ligand design
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Rapid procedure for evaluation of small molecule drug-receptor interactions
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Genetic algorithms in molecular recognition and design
inferred← citeshttps://doi.org/10.1016/s0169-7439(98)00132-4openalex-snapshot
Automated docking of peptides and proteins by genetic algorithm
inferred← citeshttps://doi.org/10.1016/s0300-9084(98)80019-9openalex-snapshot
Towards structural models of molecular recognition in olfactory receptors
inferred← citeshttps://doi.org/10.1016/s0922-3487(03)23004-5openalex-snapshot
Genetic algorithms in molecular modelling: a review
inferred← citeshttps://doi.org/10.1016/s0958-1669(96)80120-0openalex-snapshot
Current computational tools for de novo ligand design
inferred← citeshttps://doi.org/10.1016/s0959-440x(96)80061-3openalex-snapshot
Computational methods for biomolecular docking
inferred← citeshttps://doi.org/10.1016/s0959-440x(96)80081-9openalex-snapshot
Modeling protein—ligand complexes
inferred← citeshttps://doi.org/10.1016/s1050-1738(96)00068-0openalex-snapshot
Computational Science New Horizons and Relevance to Pharmaceutical Design
inferred← citeshttps://doi.org/10.1016/s1093-3263(00)00042-5openalex-snapshot
Single-coordinate-driving method for molecular docking: application to modeling of guest inclusion in cyclodextrin
inferred← citeshttps://doi.org/10.1016/s1093-3263(00)00060-7openalex-snapshot
Designing targeted libraries with genetic algorithms
inferred← citeshttps://doi.org/10.1016/s1093-3263(02)00164-xopenalex-snapshot
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
inferred← citeshttps://doi.org/10.1016/s1359-6446(96)10045-3openalex-snapshot
Evolutionary and genetic methods in drug design
inferred← citeshttps://doi.org/10.1016/s1359-6446(97)01163-xopenalex-snapshot
Virtual screening—an overview
inferred← citeshttps://doi.org/10.1016/s1380-7323(01)80009-1openalex-snapshot
Monte Carlo simulations of HIV-1 protease binding dynamics and thermodynamics with ensembles of protein conformations: Incorporating protein flexibility in deciphering mechanisms of molecular recognition
inferred← citeshttps://doi.org/10.1021/acs.chemmater.1c00538openalex-snapshot
Genetic Algorithms and Machine Learning for Predicting Surface Composition, Structure, and Chemistry: A Historical Perspective and Assessment
inferred← citeshttps://doi.org/10.1021/acsomega.2c07619openalex-snapshot
MetaDOCK: A Combinatorial Molecular Docking Approach
inferred← citeshttps://doi.org/10.1021/bi962250ropenalex-snapshot
Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca2+ Positions Determined by a Genetic Algorithm
inferred← citeshttps://doi.org/10.1021/bi9825450openalex-snapshot
Nuclear Magnetic Resonance and Restrained Molecular Dynamics Studies of the Interaction of an Epidermal Growth Factor-Derived Peptide with Protein Tyrosine Phosphatase 1B,
inferred← citeshttps://doi.org/10.1021/cc049866hopenalex-snapshot
Focused Combinatorial Library Design Based on Structural Diversity, Druglikeness and Binding Affinity Score
inferred← citeshttps://doi.org/10.1021/ci049853ropenalex-snapshot
Creating Artificial Binding Pocket Boundaries To Improve the Efficiency of Flexible Ligand Docking
inferred← citeshttps://doi.org/10.1021/ci049885eopenalex-snapshot
LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters
inferred← citeshttps://doi.org/10.1021/ci050065ropenalex-snapshot
Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)
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/ci800081sopenalex-snapshot
Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method
inferred← citeshttps://doi.org/10.1021/ci800166popenalex-snapshot
Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci900212vopenalex-snapshot
Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis
inferred← citeshttps://doi.org/10.1021/ci990440dopenalex-snapshot
New Approach to Molecular Docking and Its Application to Virtual Screening of Chemical Databases
inferred← citeshttps://doi.org/10.1021/cr300314qopenalex-snapshot
Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity
inferred← citeshttps://doi.org/10.1021/ct100245nopenalex-snapshot
Modeling Protein−Ligand Binding by Mining Minima
inferred← citeshttps://doi.org/10.1021/ja011240xopenalex-snapshot
TreeDock: A Tool for Protein Docking Based on Minimizing van der Waals Energies
inferred← citeshttps://doi.org/10.1021/ja984354qopenalex-snapshot
Modeling Studies of the Interactions between the Insulin Receptor Kinase Domain and Protein Tyrosine Phosphatase 1B
inferred← citeshttps://doi.org/10.1021/jm021070eopenalex-snapshot
3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-alkylamides as a New Class of Synthetic Histone Deacetylase Inhibitors. 1. Design, Synthesis, Biological Evaluation, and Binding Mode Studies Performed through Three Different Docking Procedures
inferred← citeshttps://doi.org/10.1021/jm030990+openalex-snapshot
3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamides as a New Class of Synthetic Histone Deacetylase Inhibitors. 2. Effect of Pyrrole-C2 and/or -C4 Substitutions on Biological Activity
inferred← citeshttps://doi.org/10.1021/jm031036fopenalex-snapshot
3-(4-Aroyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides as a New Class of Synthetic Histone Deacetylase Inhibitors. 3. Discovery of Novel Lead Compounds through Structure-Based Drug Design and Docking Studies,
inferred← citeshttps://doi.org/10.1021/jm050504dopenalex-snapshot
Comparative Virtual and Experimental High-Throughput Screening for Glycogen Synthase Kinase-3β Inhibitors
inferred← citeshttps://doi.org/10.1021/jm980472copenalex-snapshot
The Role of Waters in Docking Strategies with Incremental Flexibility for Carbohydrate Derivatives: Heat-Labile Enterotoxin, a Multivalent Test Case
inferred← citeshttps://doi.org/10.1021/jp034613kopenalex-snapshot
Parameters for the Generalized Born Model Consistent with RESP Atomic Partial Charge Assignment Protocol
inferred← citeshttps://doi.org/10.1021/jp044185yopenalex-snapshot
Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics
inferred← citeshttps://doi.org/10.1021/jp993073hopenalex-snapshot
Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems
inferred← citeshttps://doi.org/10.1023/a:1007913026166openalex-snapshot
Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention
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A comparison of heuristic search algorithms for molecular docking
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:1008015827877openalex-snapshot
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
inferred← citeshttps://doi.org/10.1023/a:1008042711516openalex-snapshot
Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
inferred← citeshttps://doi.org/10.1023/a:1008066310669openalex-snapshot
DREAM++: Flexible docking program for virtual combinatorial libraries
inferred← citeshttps://doi.org/10.1023/a:1008121029716openalex-snapshot
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
inferred← citeshttps://doi.org/10.1023/a:1008158231558openalex-snapshot
Deciphering common failures in molecular docking of ligand-protein complexes
inferred← citeshttps://doi.org/10.1023/a:1008737207775openalex-snapshot
Virtual screening with solvation and ligand-induced complementarity
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferred← citeshttps://doi.org/10.1023/a:1011188704521openalex-snapshot
Protein ligand docking based on empirical method for binding affinity estimation
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Recent advances in structure-based ligand design using molecular dynamics and Monte Carlo methods.
inferred← citeshttps://doi.org/10.1023/a:1014356529909openalex-snapshot
A comparative docking study and the design of potentially selective MMP inhibitors
inferred← citeshttps://doi.org/10.1023/a:1027299602978openalex-snapshot
Receptor-based prediction of binding affinities
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/10.1038/nbt1097-1035openalex-snapshot
Artificial intelligence for drug design
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/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/10.1039/9781849735377-00195openalex-snapshot
Binding Free Energy Calculation and Scoring in Small-Molecule Docking
inferred← citeshttps://doi.org/10.1039/c3cp44697bopenalex-snapshot
A rapid identification of hit molecules for target proteins via physico-chemical descriptors
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Analysis of a binding difference between the two dsRNA‐binding domains in TRBP reveals the modular function of a KR‐helix motif
inferred← citeshttps://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferred← citeshttps://doi.org/10.1073/pnas.93.17.8945openalex-snapshot
Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.
inferred← citeshttps://doi.org/10.1080/07391102.2004.10506969openalex-snapshot
A Free Energy Based Computational Pathway from Chemical Templates to Lead Compounds: A Case Study of COX-2 Inhibitors
inferred← citeshttps://doi.org/10.1080/10629360310001624006openalex-snapshot
New Fuzzy Logic Strategies for Bio-molecular Recognition
inferred← citeshttps://doi.org/10.1081/rrs-120014592openalex-snapshot
Methodology and Problems of Protein‐Ligand Docking: Case Study of Dihydroorotate Dehydrogenase, Thymidine Kinase, and Phosphodiesterase 4
inferred← citeshttps://doi.org/10.1093/bib/bbp017openalex-snapshot
FINDSITE: a combined evolution/structure-based approach to protein function prediction
inferred← citeshttps://doi.org/10.1093/bib/bbp063openalex-snapshot
Molecular networks for the study of TCM Pharmacology
inferred← citeshttps://doi.org/10.1093/protein/12.8.639openalex-snapshot
Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search
inferred← citeshttps://doi.org/10.1100/2012/691579openalex-snapshot
Novel Computational Methodologies for Structural Modeling of Spacious Ligand Binding Sites of G-Protein-Coupled Receptors: Development and Application to Human Leukotriene B4 Receptor
inferred← citeshttps://doi.org/10.1101/006833openalex-snapshot
A BRIEF SURVEY ON BIO INSPIRED OPTIMIZATION ALGORITHMS FOR MOLECULAR DOCKING
inferred← citeshttps://doi.org/10.1109/4233.870033openalex-snapshot
A family competition evolutionary algorithm for automated docking of flexible ligands to proteins
inferred← citeshttps://doi.org/10.1109/cec.2001.934429openalex-snapshot
Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking
inferred← citeshttps://doi.org/10.1109/tai.1998.744861openalex-snapshot
Molecular binding in structure-based drug design: a case study of the population-based annealing genetic algorithms
inferred← citeshttps://doi.org/10.1109/tsmcc.2005.855515openalex-snapshot
Evolutionary computation in bioinformatics: a review
inferred← citeshttps://doi.org/10.1110/ps.8.6.1342openalex-snapshot
The crystal structure of a bacterial, bifunctional 5, 10 methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2012.01403.xopenalex-snapshot
Combined Pharmacophore and 3D‐QSAR Study on A Series of Staphylococcus aureus Sortase A inhibitors
inferred← citeshttps://doi.org/10.11131/2016/101202openalex-snapshot
Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors
inferred← citeshttps://doi.org/10.1128/jvi.78.6.3123-3132.2004openalex-snapshot
Crystal Structures of a Multidrug-Resistant Human Immunodeficiency Virus Type 1 Protease Reveal an Expanded Active-Site Cavity
inferred← citeshttps://doi.org/10.1139/bcb-77-5-469openalex-snapshot
Structure, modelling, and molecular dynamics studies of the inhibition of protein tyrosine phosphatase 1B by sulfotyrosine peptides
inferred← citeshttps://doi.org/10.1139/v06-012openalex-snapshot
LGA-Dock/EM-Dock Exploring Lamarckian genetic algorithms and energy-based local search for ligandreceptor docking
inferred← citeshttps://doi.org/10.1145/1143997.1144287openalex-snapshot
Multi-objective optimisation of the protein-ligand docking problem in drug discovery
inferred← citeshttps://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferred← citeshttps://doi.org/10.1155/2021/8853056openalex-snapshot
An Updated Review of Computer‐Aided Drug Design and Its Application to COVID‐19
inferred← citeshttps://doi.org/10.11606/t.76.2018.tde-17092018-104828openalex-snapshot
Métodos híbridos em docagem molecular: implementação, validação e aplicação
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s17-s7openalex-snapshot
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
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