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). 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. CONTACT: pablo@chaconlab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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). 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. CONTACT: pablo@chaconlab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Iain D Nicholl; Tsutomu Matsui; Thomas M Weiss; Christopher B Stanley; William T Heller; Anne Martel; Bela Farago; David J E Callaway; Zimei Bu Journal: Biophys J Date: 2018-07-11 Impact factor: 4.033
Authors: José Ramón López-Blanco; José I Aliaga; Enrique S Quintana-Ortí; Pablo Chacón Journal: Nucleic Acids Res Date: 2014-04-25 Impact factor: 16.971
Authors: Hyunwook Lee; Heather M Callaway; Javier O Cifuente; Carol M Bator; Colin R Parrish; Susan L Hafenstein Journal: Proc Natl Acad Sci U S A Date: 2019-09-23 Impact factor: 11.205