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.

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

Laboratory of Bioinformatics and Systems Biology Centre of New Technologies University of Warsaw 02 089 Warsaw Poland

National Centre for Biomolecular Research Faculty of Science and CEITEC Central European Institute of Technology Masaryk University Brno 625 00 Brno Bohunice Czech Republic

Zobrazit více v PubMed

Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr , Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The Protein Data Bank: a computer‐based archival file for macromolecular structures. J Mol Biol 112:535–542. PubMed

Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (1997) PDBsum: a Web‐based database of summaries and analyses of all PDB structures. Trends Biochem Sci 22:488–490. PubMed

Stampf DR, Felder CE, Sussman JL (1995) PDBbrowse–a graphics interface to the Brookhaven Protein Data Bank. Nature 374:572–574. PubMed

Peitsch MC, Wells TN, Stampf DR, Sussman JL (1995) The Swiss‐3DImage collection and PDB‐Browser on the World‐Wide Web. Trends Biochem Sci 20:82–84. PubMed

Suhnel J (1996) Image library of biological macromolecules. Comput Appl Biosci 12:227–229. PubMed

Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540. PubMed

Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (1997) CATH: a hierarchic classification of protein domain structures. Structure 5:1093–1108. PubMed

Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29:221–222. PubMed PMC

Laskowski RA, Chistyakov VV, Thornton JM (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:D266–D268. PubMed PMC

Laskowski RA (2009) PDBsum new things. Nucleic Acids Res 37:D355–D359. PubMed PMC

de Beer TA, Berka K, Thornton JM, Laskowski RA (2014) PDBsum additions. Nucleic Acids Res 42:D292–D296. PubMed PMC

Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301–D303. PubMed PMC

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242. PubMed PMC

Rose PW, Prlic A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45:D271–D281. PubMed PMC

Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, et al. (2016) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44:D385–D395. PubMed PMC

Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA (2017) A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res 45:3785–3799. PubMed PMC

DeLano WL (2002) The PyMOL Molecular Graphics System. Palo Alto, CA: DeLano Scientific.

Rego N, Koes D (2015) 3Dmol.js: molecular visualization with WebGL. Bioinformatics 31:1322–1324. PubMed PMC

Sayle RA, Milner‐White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 20:374. PubMed

Herraez A (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 34:255–261. PubMed

Gille C, Frommel C (2001) STRAP: editor for structural alignments of proteins. Bioinformatics 17:377–378. PubMed

Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13:323–330, 307–308. PubMed

Laskowski RA, Luscombe NM, Swindells MB, Thornton JM (1996) Protein clefts in molecular recognition and function. Protein Sci 5:2438–2452. PubMed PMC

Milburn D, Laskowski RA, Thornton JM (1998) Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Eng 11:855–859. PubMed

Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63–98. PubMed

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador‐Vegas A, et al. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285. PubMed PMC

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, et al. (2015) CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 43:D376–D381. PubMed PMC

Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG (2014) SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res 42:D310–D314. PubMed PMC

McDonald IK, Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777–793. PubMed

Wallace AC, Laskowski RA (1995) Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein‐ligand interactions. Protein Eng 8:127–134. PubMed

Luscombe NM, Laskowski RA, Thornton JM (1997) NUCPLOT: a program to generate schematic diagrams of protein‐nucleic acid interactions. Nucleic Acids Res 25:4940–4945. PubMed PMC

Hutchinson EG, Thornton JM (1996) PROMOTIF–a program to identify and analyze structural motifs in proteins. Protein Sci 5:212–220. PubMed PMC

Hutchinson EG, Thornton JM (1990) HERA–a program to draw schematic diagrams of protein secondary structures. Proteins 8:203–212. PubMed

Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK ‐ a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291.

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361. PubMed PMC

Tamuri AU, Laskowski RA (2010) ArchSchema: a tool for interactive graphing of related Pfam domain architectures. Bioinformatics 26:1260–1261. PubMed

The UniProt C (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169. PubMed PMC

Sehnal D, Svobodova Varekova R, Berka K, Pravda L, Navratilova V, Banas P, Ionescu CM, Otyepka M, Koca J (2013) MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform 5:39. PubMed PMC

Varekova RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horsky V, Wimmerova M, Koca J (2014) MotiveValidator: interactive web‐based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res 42:W227–W233. PubMed PMC

Sehnal D, Svobodova Varekova R, Pravda L, Ionescu CM, Geidl S, Horsky V, Jaiswal D, Wimmerova M, Koca J (2015) ValidatorDB: database of up‐to‐date validation results for ligands and non‐standard residues from the Protein Data Bank. Nucleic Acids Res 43:D369–D375. PubMed PMC

Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ (2013) SIFTS: structure integration with function, taxonomy and sequences resource. Nucleic Acids Res 41:D483–D489. PubMed PMC

Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, Wilson M, Neveu V, et al. (2014) DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 42:D1091–D1097. PubMed PMC

Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:W89–W93. PubMed PMC

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education

Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells

Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts

Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants

MISCAST: MIssense variant to protein StruCture Analysis web SuiTe