ArticleBioinformatics (Oxford, England)2020
LightDock goes information-driven.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Molecular architecture of the human citrate synthase-malate dehydrogenase 2 metabolon.Acta crystallographica. Section D, Structural biology · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Investigating Escherichia coli Colicin E9 immunity protein interactions with DNA gyrase of Pseudomonas aeruginosa: advanced computational approach for developing novel antimicrobial strategies.Scientific reports · 2026Article
- Development and Functional Characterization of Recombinant Mussel Adhesive Protein for Anti-Oxidative and Anti-Aging Therapeutic Applications.International journal of molecular sciences · 2025Article
- Molecular Architecture of the human Citrate Synthase-Malate Dehydrogenase 2 metabolon.bioRxiv : the preprint server for biology · 2025Article
- The N-terminal domain of COMPANION OF CELLULOSE SYNTHASE1 promotes microtubule array formation in Arabidopsis.Plant physiology · 2025Article
- TARPγ2-Derived Peptide Enhances Early-Phase Long-Term Potentiation and Impairs Memory Retention in Male Rats.Brain sciences · 2025Article
- High-affinity optimization potential of the virus neutralizing antibody with twin cysteine-stabilized complementarity-determining region 3.Frontiers in cellular and infection microbiology · 2025Article
- Investigating and evaluating potential antigen binding sites for monoclonal anti-HER2 antibodies: The LightDock approach.Computational and structural biotechnology journal · 2025Article
- Challenges in predicting PROTAC-mediated protein-protein interfaces with AlphaFold reveal a general limitation on small interfaces.Bioinformatics advances · 2025Article
- Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes.Genomics, proteomics & bioinformatics · 2024Review
- Open-Source Machine Learning in Computational Chemistry.Journal of chemical information and modeling · 2023Review
- The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.Nucleic acids research · 2023Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- Information-Driven Docking for TCR-pMHC Complex Prediction.Frontiers in immunology · 2021Article
- Integrative modeling of membrane-associated protein assemblies.Nature communications · 2020Article
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe use of experimental information has been demonstrated to increase the success rate of computational macromolecular docking. Many methods use information to post-filter the simulation output while others drive the simulation based on experimental restraints, which can become problematic for more complex scenarios such as multiple binding interfaces.
resultsWe present a novel method for including interface information into protein docking simulations within the LightDock framework. Prior to the simulation, irrelevant regions from the receptor are excluded for sampling (filter of initial swarms) and initial ligand poses are pre-oriented based on ligand input information. We demonstrate the applicability of this approach on the new 55 cases of the Protein-Protein Docking Benchmark 5, using different amounts of information. Even with incomplete or incorrect information, a significant improvement in performance is obtained compared to blind ab initio docking. AVAILABILITY AND IMPLEMENTATION: The software is supported and freely available from https://github.com/brianjimenez/lightdock and analysis data from https://github.com/brianjimenez/lightdock_bm5. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.