ArticleBMC bioinformatics2013
ΔΔPT: a comprehensive toolbox for the analysis of protein motion.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Computational identification of conserved dengue virus envelope protein epitopes for vaccine design and immunodiagnostic platform.Scientific reports · 2026Article
- Design and Characterization of a Cell-Penetrating Peptide Derived from the SOX2 Transcription Factor.International journal of molecular sciences · 2021Article
- BANΔIT: B'-Factor Analysis for Drug Design and Structural Biology.Molecular informatics · 2021Article
- Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease.Journal of the Royal Society, Interface · 2021Article
- The 'allosteron' model for entropic allostery of self-assembly.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Folding cooperativity and allosteric function in the tandem-repeat protein class.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?Biophysical journal · 2015Article
- The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein.The Journal of biological chemistry · 2015Article
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- Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.PLoS biology · 2013Article
- Global low-frequency motions in protein allostery: CAP as a model system.Biophysical reviewsArticle
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNormal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies.
resultsΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies.
conclusionsThis toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software.
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Registered trials
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