{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T18:21:16Z","timestamp":1735582876900},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,15]]},"abstract":"Abstract<\/jats:title>Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC).<\/jats:p>Results: Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency.<\/jats:p>Contact: \u00a0pablo@chaconlab.org<\/jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr497","type":"journal-article","created":{"date-parts":[[2011,8,28]],"date-time":"2011-08-28T00:36:05Z","timestamp":1314491765000},"page":"2843-2850","source":"Crossref","is-referenced-by-count":216,"title":["iMod: multipurpose normal mode analysis in internal coordinates"],"prefix":"10.1093","volume":"27","author":[{"given":"Jos\u00e9 Ram\u00f3n","family":"Lop\u00e9z-Blanco","sequence":"first","affiliation":[{"name":"1 Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain and 2Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, USA"}]},{"given":"Jos\u00e9 Ignacio","family":"Garz\u00f3n","sequence":"additional","affiliation":[{"name":"1 Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain and 2Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, USA"}]},{"given":"Pablo","family":"Chac\u00f3n","sequence":"additional","affiliation":[{"name":"1 Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain and 2Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,8,27]]},"reference":[{"key":"2023012512011580500_B1","doi-asserted-by":"crossref","first-page":"3341","DOI":"10.1002\/prot.22841","article-title":"Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses","volume":"78","author":"Ahmed","year":"2010","journal-title":"Proteins Struct. 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