A web app to trace conformational transitions in proteins. GOdMD uses the fast CG dMD algorithm coupled to two biasing methods: (i) metadynamics adapted to follow proteins easiest deformation pattern, and (ii) a Metropolis-based Maxwell Demon algorithm. The method is fast and, contrary to many other approaches, always finds a smooth transition path when tested in a large dataset of transitions.
Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain; National Institute of Bioinformatics, University of Barcelona, Barcelona, Spain, Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
GOdMD funding source(s)
This work was supported by Ministerio de Economia y Competitividad, Spain; the European Research Council (ERC-Advanced Grant (BIO2012-32868), the Instituto Nacional de Bioinformatica, the Consolider E-Science Project, Framework VII Scalalife Project, Fundacion Marcelino Botin.