title: Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins.
abstract: Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
authors.affiliation: Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Cossio-Pérez
authors.affiliation: Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina.
authors.forename: Juliana
authors.identifier: 0000-0002-0761-0253
authors.initials: J
authors.lastname: Palma
authors.affiliation: Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Pierdominici-Sottile
mesh_terms: D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism*; D025341:Principal Component Analysis; D011487:Protein Conformation
chemical_list: D009113:Muramidase