On the public citation graph

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size

https://doi.org/10.1021/ci9002415
0 signed · 61 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/chin.200642205openalex-snapshot
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large‐Scale Survey on the Retrieval of Protein‐Bound Ligand Conformations.
inferredcites →https://doi.org/10.1002/jcc.540100804openalex-snapshot
Validation of the general purpose tripos 5.2 force field
inferredcites →https://doi.org/10.1002/jcc.540111012openalex-snapshot
Automated conformational analysis: Directed conformational search using the A* algorithm
inferredcites →https://doi.org/10.1002/jcc.540160205openalex-snapshot
Poling: Promoting conformational variation
inferredcites →https://doi.org/10.1007/bf00119865openalex-snapshot
FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure
inferredcites →https://doi.org/10.1007/bf00123666openalex-snapshot
Flexibases: A way to enhance the use of molecular docking methods
inferredcites →https://doi.org/10.1007/bf00123667openalex-snapshot
A fast and efficient method to generate biologically relevant conformations
inferredcites →https://doi.org/10.1007/bf00124464openalex-snapshot
Placement of medium-sized molecular fragments into active sites of proteins
inferredcites →https://doi.org/10.1007/bf01533070openalex-snapshot
ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0898-5529(90)90156-3openalex-snapshot
Automatic generation of 3D-atomic coordinates for organic molecules
inferredcites →https://doi.org/10.1016/0898-5529(90)90162-2openalex-snapshot
An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
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/j.jmb.2005.12.012openalex-snapshot
Conformational Diversity of Ligands Bound to Proteins
inferredcites →https://doi.org/10.1016/j.str.2008.09.007openalex-snapshot
Structural Basis for Catalytic and Inhibitory Mechanisms of Human Prostaglandin Reductase PTGR2
inferredcites →https://doi.org/10.1016/j.str.2009.02.010openalex-snapshot
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
inferredcites →https://doi.org/10.1016/s0065-7743(08)61374-3openalex-snapshot
Chapter 29 Pharmacophoric Pattern Searching and Receptor Mapping
inferredcites →https://doi.org/10.1021/ci00002a004openalex-snapshot
The development of versions 3 and 4 of the Cambridge Structural Database System
inferredcites →https://doi.org/10.1021/ci010366aopenalex-snapshot
Is There a Difference between Leads and Drugs? A Historical Perspective
inferredcites →https://doi.org/10.1021/ci060084gopenalex-snapshot
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations
inferredcites →https://doi.org/10.1021/ci060094hopenalex-snapshot
Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations
inferredcites →https://doi.org/10.1021/ci9000212openalex-snapshot
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
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/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1023/a:1008007507641openalex-snapshot
Conformational energy penalties of protein-bound ligands
inferredcites →https://doi.org/10.1023/a:1016320106741openalex-snapshot
Can we separate active from inactive conformations?
inferredcites →https://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
inferredcites →https://doi.org/10.1074/jbc.m403319200openalex-snapshot
Structural Basis for the Autoinhibition and STI-571 Inhibition of c-Kit Tyrosine Kinase
inferredcites →https://doi.org/10.1074/jbc.m608410200openalex-snapshot
X-ray Crystal Structures of the Estrogen-related Receptor-γ Ligand Binding Domain in Three Functional States Reveal the Molecular Basis of Small Molecule Regulation
inferredcites →https://doi.org/10.1093/bioinformatics/bth214openalex-snapshot
Ligand Depot: a data warehouse for ligands bound to macromolecules
inferredcites →https://doi.org/10.1186/1471-2105-7-293openalex-snapshot
Representation of target-bound drugs by computed conformers: implications for conformational libraries
inferredcites →https://doi.org/10.1186/1471-2105-9-184openalex-snapshot
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
inferredcites →https://doi.org/10.1371/journal.pone.0000820openalex-snapshot
Preference of Small Molecules for Local Minimum Conformations when Binding to Proteins

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9783527806539.ch6hopenalex-snapshot
Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1002/cmdc.201300242openalex-snapshot
CONFECT: Conformations from an Expert Collection of Torsion Patterns
inferred← citeshttps://doi.org/10.1002/cmdc.201300481openalex-snapshot
In silico Design, Synthesis, and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV‐1 Replication
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/10.1016/b978-0-12-821748-1.00001-4openalex-snapshot
Impact of chemoinformatics approaches and tools on current chemical research
inferred← citeshttps://doi.org/10.1016/j.ddtec.2010.10.003openalex-snapshot
Conformations and 3D pharmacophore searching
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.11.075openalex-snapshot
NAOMInext – Synthetically feasible fragment growing in a structure-based design context
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108434openalex-snapshot
Application of computational methods for class A GPCR Ligand discovery
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.0c00025openalex-snapshot
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01309openalex-snapshot
Molecular Gas-Phase Conformational Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00654openalex-snapshot
Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00697openalex-snapshot
Knowledge-Based Conformer Generation Using the Cambridge Structural Database
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00704openalex-snapshot
Conformator: A Novel Method for the Generation of Conformer Ensembles
inferred← citeshttps://doi.org/10.1021/ci100015jopenalex-snapshot
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
inferred← citeshttps://doi.org/10.1021/ci100466hopenalex-snapshot
Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching
inferred← citeshttps://doi.org/10.1021/ci2002318openalex-snapshot
TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations
inferred← citeshttps://doi.org/10.1021/ci2005274openalex-snapshot
Comparative Analysis of Pharmacophore Screening Tools
inferred← citeshttps://doi.org/10.1021/ci200528dopenalex-snapshot
Recognizing Pitfalls in Virtual Screening: A Critical Review
inferred← citeshttps://doi.org/10.1021/ci400510eopenalex-snapshot
Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1093/bib/bbx030openalex-snapshot
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges
inferred← citeshttps://doi.org/10.1186/1758-2946-4-s1-p14openalex-snapshot
A flexible-hydrogen interaction model for protein-ligand docking
inferred← citeshttps://doi.org/10.1186/s13321-017-0216-0openalex-snapshot
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?
inferred← citeshttps://doi.org/10.1517/17460441.2010.513711openalex-snapshot
Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
inferred← citeshttps://doi.org/10.4155/fmc-2018-0400openalex-snapshot
Energy Windows for Computed Compound Conformers: Covering Artefacts Or Truly Large Reorganization Energies?
inferred← citeshttps://doi.org/10.4155/fmc.10.244openalex-snapshot
Modeling Approaches for Ligand-Based 3D Similarity
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.