BMC Struct Biol. 2009 May 1;9:27.

PTools: an opensource molecular docking library.

Saladin A, Fiorucci S, Poulain P, Prévost C, Zacharias M.

Source

Computational Biology, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany. adrien.saladin@ibpc.fr

Abstract

BACKGROUND:

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application.

RESULTS:

We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure.

CONCLUSION:

The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

PMID:: 19409097; [PubMed - indexed for MEDLINE]
PMCID: PMC2685806

Free PMC Article

Images from this publication.See all images (2) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Related citations

Biskit--a software platform for structural bioinformatics. [Bioinformatics. 2007]
Biskit--a software platform for structural bioinformatics.
Grünberg R, Nilges M, Leckner J. Bioinformatics. 2007 Mar 15; 23(6):769-70. Epub 2007 Jan 18.
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. [Bioinformatics. 2006]
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock.
Vaqué M, Arola A, Aliagas C, Pujadas G. Bioinformatics. 2006 Jul 15; 22(14):1803-4. Epub 2006 May 23.
DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. [Proteins. 2007]
DOCKGROUND system of databases for protein recognition studies: unbound structures for docking.
Gao Y, Douguet D, Tovchigrechko A, Vakser IA. Proteins. 2007 Dec 1; 69(4):845-51.
Review A library of efficient bioinformatics algorithms. [Appl Bioinformatics. 2003]
Review A library of efficient bioinformatics algorithms.
Della Vedova G, Dondi R. Appl Bioinformatics. 2003; 2(2):117-21.
Review Recent progress and future directions in protein-protein docking. [Curr Protein Pept Sci. 2008]
Review Recent progress and future directions in protein-protein docking.
Ritchie DW. Curr Protein Pept Sci. 2008 Feb; 9(1):1-15.

See reviews... See all...

Cited by 3 PubMed Central articles

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking. [Int J Mol Sci. 2011]
Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking.
Bastard K, Saladin A, Prévost C. Int J Mol Sci. 2011 Feb 22; 12(2):1316-33. Epub 2011 Feb 22.
How cations can assist DNase I in DNA binding and hydrolysis. [PLoS Comput Biol. 2010]
How cations can assist DNase I in DNA binding and hydrolysis.
Guéroult M, Picot D, Abi-Ghanem J, Hartmann B, Baaden M. PLoS Comput Biol. 2010 Nov 18; 6(11):e1001000. Epub 2010 Nov 18.
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. [Nucleic Acids Res. 2010]
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.
Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C. Nucleic Acids Res. 2010 Oct; 38(19):6313-23. Epub 2010 May 27.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

PTools: an opensource molecular docking library.
PTools: an opensource molecular docking library.
BMC Struct Biol. 2009 May 1 ;9:27.

PubMed
Migration matrices and surnames in populations with different isolation patterns...
Migration matrices and surnames in populations with different isolation patterns: Val di Lima (Italian Apennines), Val di Sole (Italian Alps), and La Cabrera (Spain).
Am J Hum Biol. 2006 Sep-Oct ;18(5):676-90.

PubMed
Polyadenylation of rRNA in Saccharomyces cerevisiae.
Polyadenylation of rRNA in Saccharomyces cerevisiae.
Proc Natl Acad Sci U S A. 2004 Jun 8 ;101(23):8581-6. Epub 2004 Jun 1 .

PubMed
CT-guided percutaneous catheter drainage in necrotizing pancreatitis: outcomes a...
CT-guided percutaneous catheter drainage in necrotizing pancreatitis: outcomes among patients discharged with drains in place.
J Vasc Interv Radiol. 2008 Jul ;19(7):1002-6. Epub 2008 Apr 18 .

PubMed
Focus on embryonal malignancies.
Focus on embryonal malignancies.
Cancer Cell. 2002 Dec ;2(6):447-50.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: