ArticleNucleic acids research2013
PELE web server: atomistic study of biomolecular systems at your fingertips.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Molecular Insights into the Activation of a Fungal Copper Radical Oxidase by Peroxidases.Chem & bio engineering · 2026Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Tuning Selectivity in CalA Lipase: Beyond Tunnel Engineering.Biochemistry · 2023Article
- Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level.Journal of computer-aided molecular design · 2022Article
- OMN6 a novel bioengineered peptide for the treatment of multidrug resistant Gram negative bacteria.Scientific reports · 2021Article
- FDA-Approved Drugs Efavirenz, Tipranavir, and Dasabuvir Inhibit Replication of Multiple Flaviviruses in Vero Cells.Microorganisms · 2020Article
- Monte Carlo simulations using PELE to identify a protein-protein inhibitor binding site and pose.RSC advances · 2020Article
- New opportunities for designing effective small interfering RNAs.Scientific reports · 2019Article
- GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm.International journal of molecular sciences · 2019Article
- Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.Nature communications · 2019Article
- Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock.Frontiers in chemistry · 2019Article
- Kauniolide synthase is a P450 with unusual hydroxylation and cyclization-elimination activity.Nature communications · 2018Article
- Small molecule inhibits α-synuclein aggregation, disrupts amyloid fibrils, and prevents degeneration of dopaminergic neurons.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.Journal of chemical theory and computation · 2018Article
- Escape of Tick-Borne Flavivirus from 2'-Journal of virology · 2017Article
- Adaptive simulations, towards interactive protein-ligand modeling.Scientific reports · 2017Article
- Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case.Scientific reports · 2017Article
- Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions.Biophysical journal · 2017Article
- A resorcinarene for inhibition of Aβ fibrillation.Chemical science · 2017Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
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.