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Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules

https://doi.org/10.1021/ci500358p
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What this work says

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

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Validation of the general purpose tripos 5.2 force field
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A fast and efficient method to generate biologically relevant conformations
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A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
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The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures
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Simulation Analysis of Experimental Design Strategies for Screening Random Compounds as Potential New Drugs and Agrochemicals
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Retrieval of Crystallographically-Derived Molecular Geometry Information
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Molecular Modeling Studies Focused on 5-HT7 versus 5-HT1A Selectivity. Discovery of Novel Phenylpyrrole Derivatives with High Affinity for 5-HT7 Receptors
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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
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Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
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Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching
inferredcites →https://doi.org/10.1021/ci200439dopenalex-snapshot
Validating and Understanding Ring Conformations Using Small Molecule Crystallographic Data
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Freely Available Conformer Generation Methods: How Good Are They?
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Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
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/ci7002494openalex-snapshot
Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis
inferredcites →https://doi.org/10.1021/ci900238aopenalex-snapshot
Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss
inferredcites →https://doi.org/10.1021/jm3016816openalex-snapshot
Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide
inferredcites →https://doi.org/10.1021/jp052465nopenalex-snapshot
Challenges of Crystal Structure Prediction of Diastereomeric Salt Pairs
inferredcites →https://doi.org/10.1039/c1ce05362kopenalex-snapshot
Crystal structure of propylthiouracil determined using high-resolution synchrotron X-ray powder diffraction
inferredcites →https://doi.org/10.1039/c2ce25585eopenalex-snapshot
Systematic conformational bias in small-molecule crystal structures is rare and explicable
inferredcites →https://doi.org/10.1039/dt98900000s1openalex-snapshot
Supplement. Tables of bond lengths determined by X-ray and neutron diffraction. Part 2. Organometallic compounds and co-ordination complexes of the d- and f-block metals
inferredcites →https://doi.org/10.1039/p298700000s1openalex-snapshot
Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds
inferredcites →https://doi.org/10.1107/s0021889806042117openalex-snapshot
DASH : a program for crystal structure determination from powder diffraction data
inferredcites →https://doi.org/10.1107/s0021889808007279openalex-snapshot
Structure refinement: some background theory and practical strategies
inferredcites →https://doi.org/10.1107/s0021889812040113openalex-snapshot
TALP: a multisolution direct-space strategy for solving molecular crystals from powder diffraction data based on restrained least squares
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/s0108768112045636openalex-snapshot
The polymorphs of ROY: application of a systematic crystal structure prediction technique
inferredcites →https://doi.org/10.1107/s090744490804362xopenalex-snapshot
Structure validation in chemical crystallography
inferredcites →https://doi.org/10.1107/s0907444911050359openalex-snapshot
Implementing an X-ray validation pipeline for the Protein Data Bank
inferredcites →https://doi.org/10.1107/s0907444911056058openalex-snapshot
Exploiting structure similarity in refinement: automated NCS and target-structure restraints inBUSTER
inferredcites →https://doi.org/10.1107/s0907444912000200openalex-snapshot
Handling ligands with Coot
inferredcites →https://doi.org/10.1107/s1399004713030071openalex-snapshot
Ligand placement based on prior structures: the guided ligand-replacement method
inferredcites →https://doi.org/10.1186/1758-2946-3-8openalex-snapshot
Confab - Systematic generation of diverse low-energy conformers

What points at this work

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

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Stereoelectronic Effects with Donor and Acceptor Separated by a Single Bond Bridge
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Monomer Choice Influences N-Acryloyl Amino Acid Grafter Conversion via Protease Catalysis
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Knowledge-Based Approaches to H-Bonding Patterns in Heterocycle-1-Carbohydrazoneamides
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Liquid Nicotine Tamed in Solid Forms by Cocrystallization
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A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts
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Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences
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Benchmark of Generic Shapes for Macrocycles
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Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures
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Quantifying Molecular Flexibility Using Crystallographically Accessible Conformational Space
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Knowledge-Based Conformer Generation Using the Cambridge Structural Database
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Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations
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Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug Discovery
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Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules
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Rational Design of Stapled Covalent Peptide Modifiers of Oncoprotein E6 from Human Papillomavirus
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