PDBsum: Structural summaries of PDB entries

2017/09/06 by Roman A. Laskowski, Jagoda Jabłońska, Lukáš Pravda +2 · 16 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · #Bioinformatics and Genomic Networks #Enzyme Structure and Function #Protein Structure and Dynamics

paper · pdf · doi:10.1002/pro.3289

openalex publication_date 2017/09/06 · openalex created_date 2017/09/15 · openalex updated_date 2026/07/30

Abstract

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum.

Citations

• The protein data bank: A computer-based archival file for macromolecular structures
• PROCHECK: a program to check the stereochemical quality of protein structures

Cited by

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• Proteome mining of Yersinia Enterocolitica for drug targets and computational inhibitor identification with ADMET, anti-inflammation potential and formulation characteristics
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• Biophysical characterization of a putative antimicrobial peptide‐binding protein of Escherichia coli highlights its dual functionality
• Resveratrol and Its Metabolite as Potential Allosteric Regulators of Monoamine Oxidase A Activity in the Brain and Liver Under Chronic Predator Stress
• The crystal structure of an uncharacterized domain of P113 from Plasmodium falciparum
• Crystal structure of the S -adenosylmethionine-dependent mycolic acid synthase UmaA from Mycobacterium tuberculosis
• Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts
• Calicivirus assembly and stability are mediated by the N-terminal domain of the capsid protein with the involvement of the viral genome
• Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction
• The crystal structure of EpHTT, a hydroxycinnamoyl transferase from Echinacea purpurea
• Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection
• Revisiting D‐Acylases for D‐Amino Acid Production
• In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque

Related

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