Real-Time PyMOL Visualization for Rosetta and PyRosetta 英文参考文献.docVIP

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Real-Time PyMOL Visualization for Rosetta and PyRosetta 英文参考文献.doc

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Real-Time PyMOL Visualization for Rosetta and PyRosetta 英文参考文献

Real-TimePyMOLVisualizationforRosettaand PyRosetta EvanH.Baugh1,SergeyLyskov1,BrianD.Weitzner1,JeffreyJ.Gray1,2* 1Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America, 2Program in Molecular Biophysics,TheJohnsHopkinsUniversity,Baltimore,Maryland,UnitedStatesofAmerica Abstract Computationalstructurepredictionanddesignofproteinsandprotein-proteincomplexeshavelongbeeninaccessibleto those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualizationsolution.Severaltoolsexistforthesolepurposeofvisualizingbiomolecules;oneofthemostpopulartools, PyMOL(Schro¨dinger),isapowerful,highlyextensible,userfriendly,andattractivepackage.IntegratingRosettaandPyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solutionbasedontransmittingbiomolecularstructureandenergyinformationviaUDPsockets.RosettaandPyMOLrunas separateprocesses,therebyavoidingmanytechnicalobstacleswhilevisualizinginformationon-demandinreal-time.When Rosettadetects changesinthestructureofaprotein,newcoordinates aresentoveraUDPnetworksockettoaPyMOL instancerunningaUDPsocketlistener.PyMOLtheninterpretsanddisplaysthemolecule.Thisimplementationalsoallows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environmentforproteinstructurepredictionanddesign. Citation: Baugh EH, Lyskov S, Weitzner BD, Gray JJ (2011) Real-Time PyMOL Visualization for Rosetta and PyRosetta. PLoS ONE 6(8): e21931. doi:10.1371/ journal.pone.0021931 Editor:VladimirN.Uversky,UniversityofSouthFlorida,UnitedStatesofAmerica ReceivedApril12,2011;AcceptedJune9,2011;PublishedAugust16,2011 Copyright: ? 2011 Baugh et al. This is an open-access article distributed under th