PDBsum additions
Language English Country Great Britain, England Media print-electronic
Document type Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.
Grant support
U54 GM094585
NIGMS NIH HHS - United States
HHSN272200700058C
NIAID NIH HHS - United States
GM094585
NIGMS NIH HHS - United States
HHSN272201200026C
NIAID NIH HHS - United States
PubMed
24153109
PubMed Central
PMC3965036
DOI
10.1093/nar/gkt940
PII: gkt940
Knihovny.cz E-resources
- MeSH
- Databases, Protein * MeSH
- Genetic Variation MeSH
- Internet MeSH
- Protein Conformation * MeSH
- Humans MeSH
- Ligands MeSH
- Computer Graphics MeSH
- Proteins chemistry genetics MeSH
- Drug Design MeSH
- Cluster Analysis MeSH
- Protein Structure, Tertiary MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Names of Substances
- Ligands MeSH
- Proteins MeSH
PDBsum, http://www.ebi.ac.uk/pdbsum, is a website providing numerous pictorial analyses of each entry in the Protein Data Bank. It portrays the structural features of all proteins, DNA and ligands in the entry, as well as depicting the interactions between them. The latest features, described here, include annotation of human protein sequences with their naturally occurring amino acid variants, dynamic graphs showing the relationships between related protein domain architectures, analyses of ligand binding clusters across different experimental determinations of the same protein, analyses of tunnels in proteins and new search options.
See more in PubMed
Berman HM, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 2003;10:980. PubMed
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci. 1997;22:488–490. PubMed
Laskowski RA. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. 2001;29:221–222. PubMed PMC
Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res. 2005;33:D266–D268. PubMed PMC
Laskowski RA. Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics. 2007;23:1824–1827. PubMed
Laskowski RA. PDBsum new things. Nucleic Acids Res. 2009;37:D355–D359. PubMed PMC
1000 Genomes Project Consortium. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65. PubMed PMC
UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013;41:D43–D47. PubMed PMC
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48–D55. PubMed PMC
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O’Donovan C, Martin M, Kleywegt GJ. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 2013;41:D483–D489. PubMed PMC
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29: 308–311. PubMed PMC
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993;234:779–815. PubMed
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995;8:127–134. PubMed
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290–D301. PubMed PMC
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, et al. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res. 2013;41:D490–D498. PubMed PMC
Tamuri AU, Laskowski RA. ArchSchema: a tool for interactive graphing of related Pfam domain architectures. Bioinformatics. 2010;26:1260–1261. PubMed
Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 1995;20:374. PubMed
Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, et al. DrugBank 3.0: a comprehensive resource for’omics’ research on drugs. Nucleic Acids Res. 2011;39:D1035–D1041. PubMed PMC
Sehnal D, Svobodova Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C, Otyepka M, Koča J. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminform. 2013;5:39. PubMed PMC
Berka K, Hanak O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C, Svobodova Vařeková R, Koča J, et al. MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 2012;40:W222–W227. PubMed PMC
ChannelsDB: database of biomacromolecular tunnels and pores
PDBsum: Structural summaries of PDB entries
