title: Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.
abstract: We present a new method for estimating pathways for conformational transitions in macromolecules from the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques. The method can work with high efficiency at different levels of resolution, including the atomistic one, and can help to define initial pathways for further exploration by means of more accurate atomistic molecular dynamics simulations. The method is implemented in a freely available Web-based application accessible at http://mmb.irbbarcelona.org/MDdMD .
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Sfriso
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.
authors.forename: Agusti
authors.initials: A
authors.lastname: Emperador
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Orellana
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.|Structural Bioinformatics Node, Instituto Nacional De Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.|Computational Bioinformatics Node, Instituto Nacional De Bioinformática, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, 08034, Spain.|Departament de Bioquímica, Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647, Barcelona, 08028, Spain.
authors.forename: Josep Lluis
authors.initials: JL
authors.lastname: Gelpí
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.|Structural Bioinformatics Node, Instituto Nacional De Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.|Departament de Bioquímica, Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647, Barcelona, 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco