PLIP: fully automated protein-ligand interaction profiler

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

Abstract

The characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein-ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web. The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling.

Details

Original languageEnglish
Pages (from-to)W443–W447
JournalNucleic Acids Research
Volume43
Issue numberW1
Publication statusPublished - 1 Jul 2015
Peer-reviewedYes

External IDs

Scopus 84979851890
PubMed 25873628
PubMedCentral PMC4489249
ORCID /0000-0003-2848-6949/work/141543331

Keywords

Keywords

  • Algorithms, Enzyme Inhibitors/chemistry, Internet, Ligands, Molecular Docking Simulation/methods, Protein Conformation, Proteins/chemistry, Software