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A Comprehensive Docking Study on the Selectivity of Binding of Aromatic Compounds to Proteins

https://doi.org/10.1021/ci034052u
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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(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/(sici)1097-0134(19990701)36:1<1::aid-prot1>3.0.co;2-topenalex-snapshot
Flexible ligand docking: A multistep strategy approach
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991001)37:1<88::aid-prot9>3.0.co;2-oopenalex-snapshot
Exhaustive docking of molecular fragments with electrostatic solvation
inferredcites →https://doi.org/10.1002/(sici)1097-461x(1998)69:1<77::aid-qua10>3.0.co;2-2openalex-snapshot
Calculation of ligand binding free energies from molecular dynamics simulations
inferredcites →https://doi.org/10.1002/prot.10186openalex-snapshot
Progress toward virtual screening for drug side effects
inferredcites →https://doi.org/10.1002/prot.340200104openalex-snapshot
Predicting molecular interactions and inducible complementarity: Fragment docking of fab‐peptide complexes
inferredcites →https://doi.org/10.1006/bbrc.2002.6745openalex-snapshot
Pentapeptide Amides Interfere with the Aggregation of β-Amyloid Peptide of Alzheimer's Disease
inferredcites →https://doi.org/10.1016/0040-4020(80)80168-2openalex-snapshot
Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/s0968-0896(01)00424-2openalex-snapshot
Mapping of Possible Binding Sequences of Two Beta-Sheet Breaker Peptides on Beta Amyloid Peptide of Alzheimer's Disease
inferredcites →https://doi.org/10.1016/s1367-5931(02)00339-3openalex-snapshot
Lead discovery using molecular docking
inferredcites →https://doi.org/10.1016/s1367-5931(02)00341-1openalex-snapshot
Protein flexibility and drug design: how to hit a moving target
inferredcites →https://doi.org/10.1021/jm010927popenalex-snapshot
SAR and X-ray. A New Approach Combining Fragment-Based Screening and Rational Drug Design: Application to the Discovery of Nanomolar Inhibitors of Src SH2
inferredcites →https://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
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:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1023/a:1016307520660openalex-snapshot
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1073/pnas.062398499openalex-snapshot
Computational mapping identifies the binding sites of organic solvents on proteins
inferredcites →https://doi.org/10.1093/bioinformatics/18.7.939openalex-snapshot
Ligand-induced changes in the binding sites of proteins
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/29.1.221openalex-snapshot
PDBsum: summaries and analyses of PDB structures
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms

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.200351217openalex-snapshot
A Comprehensive Docking Study on the Selectivity of Binding of Aromatic Compounds to Proteins.
inferred← citeshttps://doi.org/10.1002/cmdc.200600251openalex-snapshot
Structure‐Based Calculation of Binding Affinities of α2A‐Adrenoceptor Agonists
inferred← citeshttps://doi.org/10.1007/s00044-011-9567-7openalex-snapshot
Pharmacophore modeling and structure-based virtual screening for a novel “switch region” target of bacterial RNA polymerase
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.01.005openalex-snapshot
5-Alkyl-2-alkylamino-6-(2,6-difluorophenylalkyl)-3,4-dihydropyrimidin-4(3H)-ones, a new series of potent, broad-spectrum non-nucleoside reverse transcriptase inhibitors belonging to the DABO family
inferred← citeshttps://doi.org/10.1016/j.febslet.2006.01.074openalex-snapshot
Blind docking of drug‐sized compounds to proteins with up to a thousand residues
inferred← citeshttps://doi.org/10.1016/j.jmb.2005.04.039openalex-snapshot
Extended Intermolecular Interactions in a Serine Protease–Canonical Inhibitor Complex Account for Strong and Highly Specific Inhibition
inferred← citeshttps://doi.org/10.1021/bi060991eopenalex-snapshot
Alternatively Spliced Exon B of Myosin Va Is Essential for Binding the Tail-Associated Light Chain Shared by Dynein
inferred← citeshttps://doi.org/10.1021/ci2002022openalex-snapshot
Drug Effect Prediction by Polypharmacology-Based Interaction Profiling
inferred← citeshttps://doi.org/10.1021/ci3001056openalex-snapshot
Contribution of 2D and 3D Structural Features of Drug Molecules in the Prediction of Drug Profile Matching
inferred← citeshttps://doi.org/10.1021/ja055804zopenalex-snapshot
Combination of a Modified Scoring Function with Two-Dimensional Descriptors for Calculation of Binding Affinities of Bulky, Flexible Ligands to Proteins
inferred← citeshttps://doi.org/10.1038/nbt999openalex-snapshot
Ligand selectivity and competition between enzymes in silico
inferred← citeshttps://doi.org/10.1080/08927020802301904openalex-snapshot
Structure-based virtual screening for glycosyltransferase51
inferred← citeshttps://doi.org/10.1186/1472-6807-10-32openalex-snapshot
Relating the shape of protein binding sites to binding affinity profiles: is there an association?
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