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Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching

https://doi.org/10.1021/ci100466h
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What this work says

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

inferredcites →https://doi.org/10.1002/9780470451854.ch12openalex-snapshot
Docking
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Conformational analysis by intersection: CONAN
inferredcites →https://doi.org/10.1002/jcc.20622openalex-snapshot
Self‐organizing superimposition algorithm for conformational sampling
inferredcites →https://doi.org/10.1002/jcc.21087openalex-snapshot
Toward accurate relative energy predictions of the bioactive conformation of drugs
inferredcites →https://doi.org/10.1002/jcc.540100804openalex-snapshot
Validation of the general purpose tripos 5.2 force field
inferredcites →https://doi.org/10.1007/s10822-007-9156-5openalex-snapshot
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
inferredcites →https://doi.org/10.1016/0968-0896(95)00031-bopenalex-snapshot
Conformational changes of small molecules binding to proteins
inferredcites →https://doi.org/10.1016/s1093-3263(02)00204-8openalex-snapshot
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
inferredcites →https://doi.org/10.1021/ci00020a039openalex-snapshot
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
inferredcites →https://doi.org/10.1021/ci060042sopenalex-snapshot
MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-ray Structures
inferredcites →https://doi.org/10.1021/ci100015jopenalex-snapshot
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
inferredcites →https://doi.org/10.1021/ci100026xopenalex-snapshot
Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
inferredcites →https://doi.org/10.1021/ci100031xopenalex-snapshot
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci6005646openalex-snapshot
Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm
inferredcites →https://doi.org/10.1021/ci700014hopenalex-snapshot
Conformational Coverage by a Genetic Algorithm: Saturation of Conformational Space
inferredcites →https://doi.org/10.1021/ci700136xopenalex-snapshot
CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration
inferredcites →https://doi.org/10.1021/ci700189sopenalex-snapshot
Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins
inferredcites →https://doi.org/10.1021/ci7002494openalex-snapshot
Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis
inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot
Protein−Ligand Docking against Non-Native Protein Conformers
inferredcites →https://doi.org/10.1021/ci9002415openalex-snapshot
Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size
inferredcites →https://doi.org/10.1021/j100785a001openalex-snapshot
van der Waals Volumes and Radii
inferredcites →https://doi.org/10.1021/ja00033a004openalex-snapshot
Computational studies of nonbonded sulfur-oxygen and selenium-oxygen interactions in the thiazole and selenazole nucleosides
inferredcites →https://doi.org/10.1021/jm030563wopenalex-snapshot
Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
inferredcites →https://doi.org/10.1021/jm900817uopenalex-snapshot
Three-Dimensional Pharmacophore Methods in Drug Discovery
inferredcites →https://doi.org/10.1021/jp953141+openalex-snapshot
Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii
inferredcites →https://doi.org/10.1023/a:1016320106741openalex-snapshot
Can we separate active from inactive conformations?
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1107/s0108768102003324openalex-snapshot
New software for searching the Cambridge Structural Database and visualizing crystal structures
inferredcites →https://doi.org/10.1107/s0108768102003890openalex-snapshot
The Cambridge Structural Database: a quarter of a million crystal structures and rising
inferredcites →https://doi.org/10.1107/s0108768109004066openalex-snapshot
Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test
inferredcites →https://doi.org/10.1107/s0108768110012048openalex-snapshot
Bond lengths in organic and metal-organic compounds revisited: X —H bond lengths from neutron diffraction data
inferredcites →https://doi.org/10.1107/s0108768193000709openalex-snapshot
A database study of nonbonded intramolecular sulfur–nucleophile contacts

What points at this work

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

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New Types of Descriptors and Models in QSAR/QSPR
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Outside‐binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1
inferred← citeshttps://doi.org/10.1002/jcc.22996openalex-snapshot
Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.14829-2openalex-snapshot
Cambridge Structural Database (CSD)
inferred← citeshttps://doi.org/10.1016/j.bmc.2013.06.056openalex-snapshot
Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation
inferred← citeshttps://doi.org/10.1016/j.bmc.2013.10.003openalex-snapshot
Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery
inferred← citeshttps://doi.org/10.1016/j.ica.2014.08.046openalex-snapshot
Iron complexes of tris(pyrazolyl)ethane ligands methylated in the 3-, 4-, and 5-positions
inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00155openalex-snapshot
A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/ci500358popenalex-snapshot
Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules
inferred← citeshttps://doi.org/10.1021/jasms.5c00078openalex-snapshot
Assigning Peptide Structure from Ion-Mobility Mass Spectrometry Collision Cross Section Data
inferred← citeshttps://doi.org/10.1039/c2ce25585eopenalex-snapshot
Systematic conformational bias in small-molecule crystal structures is rare and explicable
inferred← citeshttps://doi.org/10.1039/c4ce00452copenalex-snapshot
Which intermolecular interactions have a significant influence on crystal packing?
inferred← citeshttps://doi.org/10.1039/d1cc02611aopenalex-snapshot
Yb( iii )-catalysed syn -thioallylation of ynamides
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Adaptation of α-synuclein fibrils following multiple system atrophy transmission to mice
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Structural Studies of the Ryanodine Receptor and Its Binding Protein, Calstabin
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