ArticleBioinformatics (Oxford, England)2013
GSATools: analysis of allosteric communication and functional local motions using a structural alphabet.
Article in Bioinformatics (Oxford, England), 2013. 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.
- Allosteric Network Analysis Toolkit for Single-Domain Phosphoproteins.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conformational spread drives the evolution of the calcium-calmodulin protein kinase II.Scientific reports · 2022Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- Activation mechanism ofScience advances · 2021Article
- Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks.Journal of chemical theory and computation · 2021Article
- The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.PLoS computational biology · 2020Article
- Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM.Biophysical journal · 2020Article
- Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet.Biomolecules · 2020Article
- Article
- Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II.PLoS computational biology · 2019Article
- "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations.Scientific reports · 2018Article
- SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.PloS one · 2018Article
- Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil.PLoS computational biology · 2017Article
- Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways.Frontiers in molecular biosciences · 2017Article
- Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.PloS one · 2017Article
- PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks.PeerJ · 2017Article
- Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors.Scientific reports · 2016Article
- GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ.BMC research notes · 2016Article
- The Gearbox of the Bacterial Flagellar Motor Switch.Structure (London, England : 1993) · 2016Article
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Authors and funding
4 authors.
Funding
Abstract
motivationGSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. AVAILABILITY: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools.
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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.