ArticlePeerJ2017
PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Special Issue "Molecular Dynamics Simulations and Structural Analysis of Protein Domains (2nd Edition)".International journal of molecular sciences · 2026Article
- Impact of Ruxolitinib Interactions on JAK2 JH1 Domain Dynamics.International journal of molecular sciences · 2025Article
- A Simple Analysis of the Second (Extra) Disulfide Bridge of VMolecules (Basel, Switzerland) · 2024Article
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Molecular dynamics of the human RhD and RhAG blood group proteins.Frontiers in chemistry · 2024Article
- Evaluation of the Potential Impact of In Silico Humanization on VInternational journal of molecular sciences · 2023Article
- Structural Space of the Duffy Antigen/Receptor for Chemokines' Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia.Biomolecules · 2023Article
- General Trends of theInternational journal of molecular sciences · 2023Article
- VInternational journal of molecular sciences · 2022Review
- Analysis of Integrin αInternational journal of molecular sciences · 2022Article
- Insights into Comparative Modeling of VInternational journal of molecular sciences · 2021Article
- PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.International journal of molecular sciences · 2021Article
- Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet.Biomolecules · 2020Article
- Substitution matrix based color schemes for sequence alignment visualization.BMC bioinformatics · 2020Article
- Data set of intrinsically disordered proteins analysed at a local protein conformation level.Data in brief · 2020Article
- Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction.PeerJ · 2020Article
- Article
- iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach.Source code for biology and medicine · 2019Article
- The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate.Frontiers in molecular neuroscience · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.
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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.