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PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure
- Source :
- Bioinformatics (Oxford, England). 23(11)
- Publication Year :
- 2007
-
Abstract
- Motivation: Protein structure comparison is a fundamental problem in structural biology and bioinformatics. Two-dimensional maps of distances between residues in the structure contain sufficient information to restore the 3D representation, while maps of contacts reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of 2D maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. PROTMAP2D is a software tool for calculation of contact and distance maps based on user-defined criteria, quantitative comparison of pairs or series of contact maps (e.g. alternative models of the same protein, model versus native structure, different trajectories from molecular dynamics simulations, etc.) and visualization of the results.Availability: PROTMAP2D for Windows / Linux / MacOSX is freely available for academic users from http://genesilico.pl/protmap2d.htmContact: iamb@genesilico.plSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Protein structure database
Models, Molecular
Theoretical computer science
Computer science
Protein Conformation
Biochemistry
Molecular dynamics
User-Computer Interface
Protein structure
Protein similarity
Sequence Analysis, Protein
Computer Graphics
Computer Simulation
Representation (mathematics)
Molecular Biology
Native structure
Structure (mathematical logic)
Measure (data warehouse)
Binding Sites
Series (mathematics)
business.industry
Proteins
Pattern recognition
Computer Science Applications
Visualization
Computational Mathematics
Computational Theory and Mathematics
Structural biology
Models, Chemical
Artificial intelligence
business
Algorithms
Software
Protein Binding
Subjects
Details
- ISSN :
- 13674811
- Volume :
- 23
- Issue :
- 11
- Database :
- OpenAIRE
- Journal :
- Bioinformatics (Oxford, England)
- Accession number :
- edsair.doi.dedup.....acce137c3c275db701f2bcae000f5422