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

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          Abstract

          The 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 p K 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.

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          Most cited references 52

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          The Protein Data Bank.

          The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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            van der Waals Volumes and Radii

             A Bondi (1964)
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              The Amber biomolecular simulation programs.

              We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. (c) 2005 Wiley Periodicals, Inc.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                July 2012
                July 2012
                8 May 2012
                8 May 2012
                : 40
                : Web Server issue
                : W537-W541
                Affiliations
                1Department of Computer Science and 2Department of Computer Science and Physics, Virginia Tech, Blacksburg, VA 24061, USA
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +1 540 231 4237; Fax: +1 540 231 6075; Email: alexey@ 123456cs.vt.edu
                Article
                gks375
                10.1093/nar/gks375
                3394296
                22570416
                © The Author(s) 2012. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Pages: 5
                Categories
                Articles

                Genetics

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