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PELE web server: atomistic study of biomolecular systems at your fingertips

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein–ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational...

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Detalles Bibliográficos
Autores principales: Madadkar-Sobhani, Armin, Guallar, Victor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692087/
https://www.ncbi.nlm.nih.gov/pubmed/23729469
http://dx.doi.org/10.1093/nar/gkt454
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author Madadkar-Sobhani, Armin
Guallar, Victor
author_facet Madadkar-Sobhani, Armin
Guallar, Victor
author_sort Madadkar-Sobhani, Armin
collection PubMed
description PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein–ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE’s heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.
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spelling pubmed-36920872013-06-25 PELE web server: atomistic study of biomolecular systems at your fingertips Madadkar-Sobhani, Armin Guallar, Victor Nucleic Acids Res Articles PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein–ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE’s heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement. Oxford University Press 2013-07 2013-05-31 /pmc/articles/PMC3692087/ /pubmed/23729469 http://dx.doi.org/10.1093/nar/gkt454 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ 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 non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Articles
Madadkar-Sobhani, Armin
Guallar, Victor
PELE web server: atomistic study of biomolecular systems at your fingertips
title PELE web server: atomistic study of biomolecular systems at your fingertips
title_full PELE web server: atomistic study of biomolecular systems at your fingertips
title_fullStr PELE web server: atomistic study of biomolecular systems at your fingertips
title_full_unstemmed PELE web server: atomistic study of biomolecular systems at your fingertips
title_short PELE web server: atomistic study of biomolecular systems at your fingertips
title_sort pele web server: atomistic study of biomolecular systems at your fingertips
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692087/
https://www.ncbi.nlm.nih.gov/pubmed/23729469
http://dx.doi.org/10.1093/nar/gkt454
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