Literature DB >> 15534698

BioSimGrid: towards a worldwide repository for biomolecular simulations.

Kaihsu Tai1, Stuart Murdock, Bing Wu, Muan Hong Ng, Steven Johnston, Hans Fangohr, Simon J Cox, Paul Jeffreys, Jonathan W Essex, Mark S P Sansom.   

Abstract

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

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Year:  2004        PMID: 15534698     DOI: 10.1039/b411352g

Source DB:  PubMed          Journal:  Org Biomol Chem        ISSN: 1477-0520            Impact factor:   3.876


  9 in total

1.  C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.

Authors:  Fredrick Robin Devadoss Victor Paul Raj; Thomas E Exner
Journal:  J Mol Model       Date:  2014-04-12       Impact factor: 1.810

2.  Molecular dynamics trajectory compression with a coarse-grained model.

Authors:  Yi-Ming Cheng; Srinivasa Murthy Gopal; Sean M Law; Michael Feig
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2011-10-17       Impact factor: 3.710

Review 3.  Molecular dynamics: survey of methods for simulating the activity of proteins.

Authors:  Stewart A Adcock; J Andrew McCammon
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

4.  Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.

Authors:  Hanne S Antila; Tiago M Ferreira; O H Samuli Ollila; Markus S Miettinen
Journal:  J Chem Inf Model       Date:  2021-01-26       Impact factor: 4.956

5.  Towards data warehousing and mining of protein unfolding simulation data.

Authors:  Daniel Berrar; Frederic Stahl; Candida Silva; J Rui Rodrigues; Rui M M Brito; Werner Dubitzky
Journal:  J Clin Monit Comput       Date:  2005-10       Impact factor: 1.977

6.  Bookshelf: a simple curation system for the storage of biomolecular simulation data.

Authors:  Shabana Vohra; Benjamin A Hall; Daniel A Holdbrook; Syma Khalid; Philip C Biggin
Journal:  Database (Oxford)       Date:  2010-12-17       Impact factor: 3.451

7.  JGromacs: a Java package for analyzing protein simulations.

Authors:  Márton Münz; Philip C Biggin
Journal:  J Chem Inf Model       Date:  2012-01-09       Impact factor: 4.956

Review 8.  Design and application of implicit solvent models in biomolecular simulations.

Authors:  Jens Kleinjung; Franca Fraternali
Journal:  Curr Opin Struct Biol       Date:  2014-05-20       Impact factor: 6.809

Review 9.  Applications of Molecular Dynamics Simulation in Protein Study.

Authors:  Siddharth Sinha; Benjamin Tam; San Ming Wang
Journal:  Membranes (Basel)       Date:  2022-08-29
  9 in total

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