ArticleBioinformatics (Oxford, England)2019
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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The trial behind it
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Who cites it
56 citing papers in PubMed.
- Localized Rigidification and Allosteric Modulation Mechanisms of SARS-CoV-2 Spike Neutralization by Class 3 and Class 4 Antibodies at Atomic Resolution: An Integrated Computational Study of Binding, Dynamics, and Allostery.bioRxiv : the preprint server for biology · 2026Article
- Biochemical and Structural Characterization of Two-domain Glycoside Hydrolase PgaB fromACS infectious diseases · 2026Article
- Mechanisms of Binding and Immune Escape Resistance for Broadly Neutralizing Antibodies Targeting Distinct Conserved SARS-CoV-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling and Energy Landscape Analysis.International journal of molecular sciences · 2026Article
- Frustration Landscapes of Broadly Neutralizing SARS-CoV-2 Spike Antibodies Targeting Conserved Epitopes Reveal Energetic Logic of Escape-Proof and Escape-Prone Mechanisms.bioRxiv : the preprint server for biology · 2026Article
- Genetic Polymorphisms Associated with Lithium Response in Bipolar Disorder: An Integrative Review and In Silico Protein-Protein Interaction Analysis.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Anti-Inflammatory Effects of Bisacurone Isolated fromMolecules (Basel, Switzerland) · 2026Article
- Antagonist Binding Actively Disrupts Interleukin-1 Receptor Dynamics to Block Co-receptor Recruitment.Computational and structural biotechnology journal · 2026Article
- Network Pharmacology Integrated Molecular Docking Analysis Identifies Potential Phytochemicals in Stachys lavandulifolia against Polycystic Ovary Syndrome.Current pharmaceutical design · 2026Article
- Luteolin Disrupts Keratinocyte-Dendritic Cell Communication in Psoriasis by Targeting Rh Family C Glycoprotein.Mediators of inflammation · 2026Article
- Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike-Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach.bioRxiv : the preprint server for biology · 2025Article
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- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- Uracil-DNA Glycosylase fromInternational journal of molecular sciences · 2025Article
- Article
- CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.Nucleic acids research · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Integrating LC-MS/MS and In Silico Methods to Uncover Bioactive Compounds with Lipase Inhibitory Potential in the Antarctic Moss Warnstorfia fontinaliopsis.Applied biochemistry and biotechnology · 2025Article
- Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots.International journal of molecular sciences · 2025Article
- Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.Computational and structural biotechnology journal · 2024Article
- Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.Protein science : a publication of the Protein Society · 2024Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryCABS-flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse-grained protein model with the reconstruction of selected models to all-atom representation and analysis of modeling results. CABS-flex standalone is designed to allow for command-line access to the CABS computations and complete control over simulation process. CABS-flex standalone is equipped with features such as: modeling of multimeric and large-size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all-atom reconstruction parameters. With these features CABS-flex standalone can be easily incorporated into other methodologies of structural biology. AVAILABILITY AND IMPLEMENTATION: CABS-flex standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex.
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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.