ACPYPE - AnteChamber PYthon Parser interfacE

Springer Science and Business Media LLC - Tập 5 Số 1 - 2012
Alan Wilter1,2, Wim Vranken3,4
1Department of Biochemistry, University of Cambridge, Cambridge, UK
2Universal Protein Resource (UniProt), EMBL-EBI, European Bioinformatics Institute, Hinxton, UK
3Department of Structural Biology, VIB and Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
4Protein Data Bank in Europe (PDBe), EMBL-EBI, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

Tóm tắt

AbstractBackgroundACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application athttp://www.ccpn.ac.uk/acpypeand as a web portal application athttp://webapps.ccpn.ac.uk/acpype.FindingsWe verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB.ConclusionsACPYPE is a tool that simplifies the automatic generation of topology and parameters indifferent formatsfordifferentmolecular mechanics programmes, includingcalculation of partial charges, while beingobject orientedfor integration with other applications.

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Tài liệu tham khảo

Wang J, Wang W, Kollman PA, Case DA: Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graphics Model. 2006, 25 (2): 247-260. 10.1016/j.jmgm.2005.12.005.

Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C: Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct, Funct, Bioinf. 2006, 65 (3): 712-725. 10.1002/prot.21123.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093/nar/28.1.235. [http://www.pdb.org].

Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE: Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol. 2009, 19 (2): 120-127. 10.1016/j.sbi.2009.03.004.

Brunger AT: Version 1.2 of the Crystallography and NMR System. Nature Protoc. 2007, 2 (11): 2728-2733. 10.1038/nprot.2007.406.

Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM: The Xplor-NIH NMR molecular structure determination package. J Magn Reson. 2003, 160: 65-73. 10.1016/S1090-7807(02)00014-9.

Schwieters CD, Kuszewski JJ, Clore GM: Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc. 2006, 48: 47-62. 10.1016/j.pnmrs.2005.10.001.

Kleywegt GJ, Henrick K, Dodson E, van Aalten DMF: Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?. Structure. 2003, 11 (9): 1051-1059. 10.1016/S0969-2126(03)00186-2.

Schüttelkopf AW, van Aalten DMF: PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr Sect D - Biol Crystallogr. 2004, 60 (8): 1355-1363. 10.1107/S0907444904011679.

Krzeminski M, Bonvin AMJJ: The GlyCaNS toolbox and web server for the generation of complex oligosaccharide models and topologies. [http://haddock.chem.uu.nl/glycans].[Tobesubmitted].

Ribeiro AAST, Horta BAC, de Alencastro RB: MKTOP: A program for automatic construction of molecular topologies. J Braz Chem Soc. 2008, 19 (7): 1433-1435. 10.1590/S0103-50532008000700031.

Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman PA: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem. 2003, 24 (16): 1999-2012. 10.1002/jcc.10349.

Jorgensen WL, Maxwell DS, Tirado-Rives J: Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996, 118 (45): 11225-11236. 10.1021/ja9621760.

Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE: An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. J Chem Theory Comput. 2011, 7 (12): 4026-4037. 10.1021/ct200196m. [http://compbio.biosci.uq.edu.au/atb].

Oostenbrink C, Villa A, Mark A, Van Gunsteren W: A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004, 25 (13): 1656-1676. 10.1002/jcc.20090.

Ponder JW, Case DA: Force fields for protein simulations. Adv Protein Chem. 2003, 66: 27-85.

Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA: Development and testing of a General Amber Force Field. J Comput Chem. 2004, 25 (9): 1157-1174. 10.1002/jcc.20035.

Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell Jr AD: CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010, 31 (4): 671-690.

Brooks BR, Brooks III CL, MacKerell Jr AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M: CHARMM: The Biomolecular Simulation Program. J Comput Chem. 2009, 30 (10): 1545-1614. 10.1002/jcc.21287.

Sorin EJ, Pande VS: Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J. 2005, 88 (4): 2472-2493. 10.1529/biophysj.104.051938.

Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K: Scalable molecular dynamics with NAMD. J Comput Chem. 2005, 26 (16): 1781-1802. 10.1002/jcc.20289.

Guha R, Howard MT, Hutchison GR, Murray-Rust P, Rzepa H, Steinbeck C, Wegner JK, Willighagen EL: The Blue Obelisk–Interoperability in chemical informatics. J Chem Inf Model. 2006, 46 (3): 991-998. 10.1021/ci050400b.

Open Babel. [http://www.openbabel.org].

Gasteiger J, Marsili M: New model for calculating atomic charges in molecules. Tetrahedron Lett. 1978, 19 (34): 3181-3184. 10.1016/S0040-4039(01)94977-9.

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham III TE, Laughton CA, Orozco M: Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Biophysical Journal. 2007, 92 (11): 3817-3829. 10.1529/biophysj.106.097782.

Walker RC, Crowley MF, Case DA: The implementation of a fast and accurate QM/MM potential method in Amber. J Comput Chem. 2008, 29 (7): 1019-1031. 10.1002/jcc.20857.

Dupradeau FY, Cézard C, Lelong R, Stanislawiak É, Pêcher J, Delepine JC, Cieplak P: R.E.DD.B: A database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Res. 2008, 36 (Database issue): D360-D367.

RESP ESP charge Derive Home Page. [http://www.q4md-forcefieldtools.org].

YASARA AutoSMILES. [http://www.yasara.org/autosmiles].

Mobley DL, Chodera JD, Dill KA: On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys. 2006, 125 (8): 084902-1–084902–16. 10.1063/1.2221683.

ffAMBER Tool amb2gmx. [http://amber.cnsm.csulb.edu/tools.html].

Ryckaert JP, Bellemans A: Molecular-Dynamics of liquid alkanes. Faraday Discuss Chem Soc. 1978, 66: 95-106.

DeLano WL: The PyMOL Molecular Graphics System. 2002, Palo Alto, CA, USA, [http://www.pymol.org].

Berman H, Henrick K, Nakamura H, Markley JL: The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007, 35: D301-D303. 10.1093/nar/gkl971.

Sadowski J, Gasteiger J, Klebe G: Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures. J Chem Inf Comput Sci. 1994, 34 (4): 1000-1008. 10.1021/ci00020a039.

The 3D structure generator CORINA. [http://www.molecular-networks.com].

Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinás M Miguel, Ulrich EL, Markley JL, Ionides J, Laue ED: The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins: Struct, Funct, Bioinf. 2005, 59 (4): 687-696. 10.1002/prot.20449.

Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ: PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2010, 38 (Database issue): D308-D317.

Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ: PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2011, 39 (Database issue): D402-D310.

Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ: RECOORD: A recalculated coordinate database of 500+proteins from the PDB using restraints from the BioMagResBank. Proteins: Struct, Funct, Bioinf. 2005, 59 (4): 662-672. 10.1002/prot.20408.

Engh RA, Huber R: Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr Sect A. 1991, 47 (4): 392-400. 10.1107/S0108767391001071.

Doreleijers JF, Sousa da Silva AW, Krieger E, Krieger E, Nabuurs SB, Spronk CAEM, Stevens TJ, Vranken WF, Vriend G, Vuister GW: CING; an integrated residue-based structure validation program suite. [http://nmr.cmbi.ru.nl/cing].[SubmittedtoJournalofBiomolecularNMR].

Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL: The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J Biomol NMR. 2009, 45 (4): 389-396. 10.1007/s10858-009-9378-z.

ffAMBER Implementation & Validation. [http://amber.cnsm.csulb.edu/∖#validation].

Humphrey W, Dalke A, Schulten K: VMD: Visual Molecular Dynamics. J Mol Graphics. 1996, 14: 33-38. 10.1016/0263-7855(96)00018-5.

Krieger E, Koraimann G, Vriend G: Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field. Proteins: Struct, Funct, Bioinf. 2002, 47 (3): 393-402. 10.1002/prot.10104.

Schuler L, Daura X, van Gunsteren W: An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J Comput Chem. 2001, 22 (11): 1205-1218. 10.1002/jcc.1078.

Fogh RH, Boucher W, Vranken WF, Pajon A, Stevens TJ, Bhat TN, Westbrook J, Ionides JMC, Laue ED: A framework for scientific data modeling and automated software development. Bioinformatics. 2005, 21 (8): 1678-1684. 10.1093/bioinformatics/bti234.

Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M: ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics. 2007, 23 (3): 381-382. 10.1093/bioinformatics/btl589.

CcpNmr Grid Portal. [http://webapps.ccpn.ac.uk/ccpngrid].

DrugDiscovery@Home. [http://drugdiscoveryathome.com].

Yoneya M: A practical guide to molecular simulation of liquid crystals. J Jpn Liq Cryst Soc: EKISHO. 2009, 13 (3): 219-228. [http://staff.aist.go.jp/makoto-yoneya/MDforEKISHO/ekisho09July/ekisho09July2.html]. [InJapanesebutGooglecanperformafairautomatictranslation].

van der Spoel D, van Maaren PJ, Caleman C: GROMACS molecule & liquid database. Bioinformatics. 2012, 28 (5): 752-753. 10.1093/bioinformatics/bts020. [http://virtualchemistry.org].

Hess B, Kutzner C, van der Spoel D, Lindahl E: GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008, 4 (3): 435-447. 10.1021/ct700301q.

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