H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

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dc.contributor.authorAnandakrishnan, Ramuen
dc.contributor.authorAguilar, Borisen
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentPhysicsen
dc.date.accessioned2019-04-15T14:27:15Zen
dc.date.available2019-04-15T14:27:15Zen
dc.date.issued2012-07en
dc.description.abstractThe accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.en
dc.description.notesFunding open access charge: National Institutes of Health [GM076121 to A.V.O.].en
dc.description.sponsorshipNational Institutes of Health [GM076121]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gks375en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issueW1en
dc.identifier.pmid22570416en
dc.identifier.urihttp://hdl.handle.net/10919/88964en
dc.identifier.volume40en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution-NonCommercial 3.0 Unporteden
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/en
dc.subjectprotein titration curvesen
dc.subjectionizable groupsen
dc.subjectdynamics simulationsen
dc.subjectpk(a) calculationsen
dc.subjectconformational flexibilityen
dc.subjectcalculating pk(a)sen
dc.subjectproton releaseen
dc.subjectbacteriorhodopsinen
dc.subjectvaluesen
dc.subjectresiduesen
dc.titleH++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulationsen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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