ArticleJournal of chemical information and modeling2021
BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Elliptical β-barrel deformation underlies gating in VDAC1.Protein science : a publication of the Protein Society · 2026Article
- Profiling the CFTR Variant Selectivity and Off-Target Interactions of VX-121.bioRxiv : the preprint server for biology · 2026Article
- Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1.bioRxiv : the preprint server for biology · 2026Article
- Drug Repurposing: Conversion of the Peripherally Restricted HIV Protease Inhibitor Amprenavir to Potent, Selective, and CNS-Penetrant Agonists for the Cannabinoid Receptor 2.Journal of medicinal chemistry · 2026Article
- The pathway-independent positive allosteric modulator C1 allows for the identification of active YCellular and molecular life sciences : CMLS · 2026Article
- A generalizable deep learning framework for structure-based protein-ligand affinity ranking.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cache: Utilizing ultra-large library screening in Rosetta to identify novel binders of the WD-repeat domain of Leucine-Rich Repeat Kinase 2.Journal of cheminformatics · 2025Article
- FakeRotLib: Expedient Noncanonical Amino Acid Parametrization in Rosetta.Journal of chemical information and modeling · 2025Article
- Similar Binding Mode of a 5-Sulfonylthiouracil Derivative Antagonist at Chemerin Receptors CMKLR1 and GPR1.Journal of medicinal chemistry · 2025Article
- Proteostasis landscapes of cystic fibrosis variants reveal drug response vulnerability.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Proteostasis Landscapes of Cystic Fibrosis Variants Reveals Drug Response Vulnerability.bioRxiv : the preprint server for biology · 2025Article
- Parameterizing non-canonical amino acids for cyclic peptide simulations.Methods in enzymology · 2025Article
- Discovery of non-retinoid compounds that suppress the pathogenic effects of misfolded rhodopsin in a mouse model of retinitis pigmentosa.PLoS biology · 2025Article
- Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids.Journal of chemical information and modeling · 2024Article
- Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.Digital discovery · 2024Article
- MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts.Nucleic acids research · 2024Article
- Article
- MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS.bioRxiv : the preprint server for biology · 2024Article
- EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution.Chemical science · 2023Article
- General trends in the effects of VX-661 and VX-445 on the plasma membrane expression of clinical CFTR variants.Cell chemical biology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We previously described BCL::Conf, a knowledge-based conformation sampling algorithm utilizing a small molecule fragment rotamer library derived from the Cambridge Structural Database (CSD, license required), as a component of the BioChemical Library (BCL) cheminformatics toolkit. This paper describes substantial improvements made to the BCL::Conf algorithm and a transition to a rotamer library derived from molecules in the Crystallography Open Database (COD, no license required). We demonstrate the performance of the new BCL::Conf on native conformer recovery in the Platinum dataset of high-quality protein-ligand complexes. This set of 2859 structures has previously been used to assess the performance of over a dozen conformer generation algorithms, including the Conformator, Balloon, RDKit DG, ETKDG, Confab, Frog2, MultiConf-DOCK, CSD conformer generator, ConfGenX-OPSL3 force field, Omega, excalc, iCon, and MOE. These benchmarks suggest that the CSD conformer generator is at the state of the art of reported conformer generators. Our results indicate that the improved BCL::Conf significantly outperforms the CSD conformer generation algorithm at binding conformer recovery across a range of ensemble sizes and with similarly fast rates of conformer generation. BCL::Conf is now distributed with the COD-derived rotamer library and is free for academic use. The BCL can be downloaded at http://meilerlab.org/bclcommons for Windows, Linux, or Apple operating systems. BCL::Conf can now also be accessed via webserver at http://meilerlab.org/bclconf.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.