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GOdMD specifications


Unique identifier OMICS_13990
Name GOdMD
Interface Web user interface
Restrictions to use None
Input data Protein structures
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Modesto Orozco

Publication for GOdMD

GOdMD citations


Dancing through Life: Molecular Dynamics Simulations and Network Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

PLoS One
PMCID: 4664246
PMID: 26619280
DOI: 10.1371/journal.pone.0143752

[…] n subdomains IA and IIA of the NBD. This may be followed by SBD-β docking with NBD, and subsequently SBD-α binds NBD []. By using discrete molecular dynamics (dMD) simulations [,] in the framework of GOdMD approach [,] we probed conformational transitions between closed and open forms of DnaK to determine molecular catalysts of allosteric changes. In the basic dMD formalism particles move in the b […]


Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

PLoS Comput Biol
PMCID: 4619321
PMID: 26488417
DOI: 10.1371/journal.pcbi.1004568

[…] TMD differs from DIMS in that explicit forces are introduced into the system Hamiltonian whereas DIMS effectively introduces an entropic force.Maxwell-Demon discrete Molecular Dynamics [] (MDdMD) and GOdMD [] are similar in spirit and are the only two methods based on a physical dynamical model among the server-based transition path generation methods. Both are based on discrete MD combined with s […]

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GOdMD institution(s)
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.

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