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Comparison of molecular dynamics and superfamily spaces of protein domain deformation |
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| Authors: | Javier A Velázquez-Muriel Manuel Rueda Isabel Cuesta Alberto Pascual-Montano Modesto Orozco José-María Carazo |
| Affiliation: | 1. Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, 28049, Madrid, Spain 3. University of California, San Francisco, Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, 1700 4th St. UCSF/MC 2552, Byers Hall Room 503, San Francisco, CA, 94158-2330, USA 2. Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain 4. The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, Mail TPC-28, La Jolla, California, 92037, USA 9. Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, 08034, Spain 5. Departament Arquitectura de Computadores y Automática, Facultad de Ciencias Físicas, Universidad Complutense, 28040, Madrid, Spain 6. Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona, 08028, Spain 7. National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona, 08028, Spain 8. National Institute of Bioinformatics, Centro Nacional de Biotecnología, CSIC, Madrid, Spain |
| Abstract: | BackgroundIt is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). |
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