ArticleJournal of chemical information and modeling2019
BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.
Article in Journal of chemical information and modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Profiling the CFTR Variant Selectivity and Off-Target Interactions of VX-121.bioRxiv : the preprint server for biology · 2026Article
- Polypharmacology of anthelmintics at host and parasite ion channels.PLoS pathogens · 2026Article
- Development of a novel therapy for systolic heart failure.EMBO molecular medicine · 2025Article
- Identification of Novel Antileishmanial Chemotypes By High-Throughput Virtual and In Vitro Screening.Acta parasitologica · 2024Article
- MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.Protein science : a publication of the Protein Society · 2024Article
- Computer-Aided Design and Biological Evaluation of Diazaspirocyclic DACS chemical neuroscience · 2024Article
- AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening.Journal of chemical information and modeling · 2024Article
- Discovery of Protease-Activated Receptor 4 (PAR4)-Tethered Ligand Antagonists Using Ultralarge Virtual Screening.ACS pharmacology & translational science · 2024Article
- SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space.Bioinformatics (Oxford, England) · 2024Article
- ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement.ACS omega · 2022Article
- Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.Frontiers in pharmacology · 2022Article
- In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2).European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences · 2021Article
- General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps.Journal of chemical information and modeling · 2021Article
- BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.Journal of chemical information and modeling · 2021Article
- Lipocalin Blc is a potential heme-binding protein.FEBS letters · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .
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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.