ArticleNucleic acids research2017
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Mapping the Binding Hotspots and Transient Binding Pockets on V-Domain Immunoglobulin Suppressor of T Cell Activation Protein Surface.ACS omega · 2024Article
- Automated Flow Peptide Synthesis Enables Engineering of Proteins with Stabilized Transient Binding Pockets.ACS central science · 2024Article
- Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design.European biophysics journal : EBJ · 2023Review
- Structural and dynamic determinants for highly selective RET kinase inhibition reveal cryptic druggability.Journal of advanced research · 2023Article
- Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study.PloS one · 2022Article
- Finding Druggable Sites in Proteins Using TACTICS.Journal of chemical information and modeling · 2021Article
- A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics.ACS pharmacology & translational science · 2021Article
- Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2021Article
- Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals.Frontiers in bioengineering and biotechnology · 2021Review
- An up-to-date overview of computational polypharmacology in modern drug discovery.Expert opinion on drug discovery · 2020Review
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.Journal of chemical information and modeling · 2019Article
- Identification of new allosteric sites and modulators of AChE through computational and experimental tools.Journal of enzyme inhibition and medicinal chemistry · 2018Article
- P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.Journal of cheminformatics · 2018Article
Corrections and comments
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues. A standard sequence conservation score per residue or a differential score per residue, for comparing on- and off-targets, can be calculated and displayed on the binding pocket for an uploaded multiple sequence alignment file, and known protein sequence annotations can be displayed simultaneously. The TRAPP webserver is freely available at http://trapp.h-its.org.
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