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Protein−Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK)

https://doi.org/10.1021/ci900332a
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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199603)17:4<429::aid-jcc5>3.0.co;2-wopenalex-snapshot
A comparison of conformational energies calculated by several molecular mechanics methods
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<520::aid-jcc2>3.0.co;2-wopenalex-snapshot
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19971115)18:14<1812::aid-jcc10>3.0.co;2-hopenalex-snapshot
Automated flexible ligand docking method and its application for database search
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/bip.20021openalex-snapshot
Conformational studies on enkephalins using the MOLS technique
inferredcites →https://doi.org/10.1002/jcc.10295openalex-snapshot
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.21495openalex-snapshot
FireDock: Fast interaction refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.22170openalex-snapshot
Principles of flexible protein–protein docking
inferredcites →https://doi.org/10.1006/jmbi.1994.1334openalex-snapshot
Satisfying Hydrogen Bonding Potential in Proteins
inferredcites →https://doi.org/10.1006/jmbi.1995.0159openalex-snapshot
SCOP: A structural classification of proteins database for the investigation of sequences and structures
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1007/bf00124321openalex-snapshot
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
inferredcites →https://doi.org/10.1007/s10822-008-9216-5openalex-snapshot
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
inferredcites →https://doi.org/10.1016/0959-440x(95)80080-8openalex-snapshot
Ligand—protein docking and rational drug design
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/j.bbrc.2004.02.114openalex-snapshot
An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides
inferredcites →https://doi.org/10.1016/s0006-3495(03)70017-4openalex-snapshot
Enhanced Sampling of the Molecular Potential Energy Surface Using Mutually Orthogonal Latin Squares: Application to Peptide Structures
inferredcites →https://doi.org/10.1016/s0092-8674(00)81717-1openalex-snapshot
The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of This Interaction by Tamoxifen
inferredcites →https://doi.org/10.1016/s0959-440x(96)80061-3openalex-snapshot
Computational methods for biomolecular docking
inferredcites →https://doi.org/10.1016/s0969-2126(01)00276-3openalex-snapshot
The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands
inferredcites →https://doi.org/10.1016/s1074-5521(96)90256-2openalex-snapshot
Predicting the structure of protein complexes: a step in the right direction
inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
inferredcites →https://doi.org/10.1021/ci00062a008openalex-snapshot
SMILES. 2. Algorithm for generation of unique SMILES notation
inferredcites →https://doi.org/10.1021/ci970433uopenalex-snapshot
Genetic Algorithms in Conformational Analysis
inferredcites →https://doi.org/10.1021/j100194a068openalex-snapshot
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
inferredcites →https://doi.org/10.1021/jp982255topenalex-snapshot
Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization
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/b:jcam.0000004604.87558.02openalex-snapshot
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
inferredcites →https://doi.org/10.1073/pnas.022418199openalex-snapshot
A stochastic algorithm for global optimization and for best populations: A test case of side chains in proteins
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank

What points at this work

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

inferred← citeshttps://doi.org/10.1002/chin.201013208openalex-snapshot
ChemInform Abstract: Protein—Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK).
inferred← citeshttps://doi.org/10.1002/jmr.1077openalex-snapshot
Challenges and advances in computational docking: 2009 in review
inferred← citeshttps://doi.org/10.1007/128_2011_213openalex-snapshot
Application of NMR and Molecular Docking in Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-4939-2285-7_11openalex-snapshot
Computational Approaches to Developing Short Cyclic Peptide Modulators of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-4939-9504-2_5openalex-snapshot
Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1007/s00894-012-1369-4openalex-snapshot
Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK)
inferred← citeshttps://doi.org/10.1007/s00894-016-3106-xopenalex-snapshot
MOLS 2.0: software package for peptide modeling and protein–ligand docking
inferred← citeshttps://doi.org/10.1007/s00894-022-05413-3openalex-snapshot
Improved docking of peptides and small molecules in iMOLSDOCK
inferred← citeshttps://doi.org/10.1007/s10822-018-0152-8openalex-snapshot
Protein–small molecule docking with receptor flexibility in iMOLSDOCK
inferred← citeshttps://doi.org/10.1007/s12272-011-0906-5openalex-snapshot
A python-based docking program utilizing a receptor bound ligand shape: PythDock
inferred← citeshttps://doi.org/10.1007/s12551-010-0039-yopenalex-snapshot
MOLS sampling and its applications in structural biophysics
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.03.008openalex-snapshot
iMOLSDOCK: Induced-fit docking using mutually orthogonal Latin squares (MOLS)
inferred← citeshttps://doi.org/10.1021/ja510636topenalex-snapshot
Computational Design and Discovery of Nanomolar Inhibitors of IκB Kinase β
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