ArticleBMC structural biology2009
PTools: an opensource molecular docking library.
Article in BMC structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails.Nucleic acids research · 2026Article
- Plasticity and Co-Factor-Dependent Structural Changes in the RecA Nucleoprotein Filament Studied by Small-Angle X-Ray Scattering (SAXS) Measurements and Molecular Modeling.Molecules (Basel, Switzerland) · 2025Article
- Structures of Oligomeric States of Tau Protein, Amyloid-β, α-Synuclein and Prion Protein Implicated in Alzheimer's Disease, Parkinson's Disease and Prionopathies.International journal of molecular sciences · 2024Review
- Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.Bio-protocol · 2021Article
- Investigation into Early Steps of Actin Recognition by the Intrinsically Disordered N-WASP Domain V.International journal of molecular sciences · 2019Article
- Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination.Nucleic acids research · 2019Article
- Benchmarking of different molecular docking methods for protein-peptide docking.BMC bioinformatics · 2019Article
- RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro.Nucleic acids research · 2018Article
- Structure of ring-shaped Aβ₄₂ oligomers determined by conformational selection.Scientific reports · 2016Article
- An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA.PloS one · 2015Article
- PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.Nucleic acids research · 2014Article
- The scoring of poses in protein-protein docking: current capabilities and future directions.BMC bioinformatics · 2013Article
- Article
- Accounting for large amplitude protein deformation during in silico macromolecular docking.International journal of molecular sciences · 2011Article
- How cations can assist DNase I in DNA binding and hydrolysis.PLoS computational biology · 2010Article
- Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMacromolecular 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.
resultsWe 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.
conclusionThe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.