The PSSH Database of Alignments Between Protein Sequences and Tertiary Structures

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Jan 10

PMID 12520061

Citations 6

Authors

Andrea Schafferhans

Joachim E W Meyer

Sean I ODonoghue

Affiliations

Soon will be listed here.

Abstract

We introduce the PSSH ('Protein Sequence-to-Structure Homologies') database derived from HSSP2, an improved version of the HSSP ('Homology-derived Secondary Structure of Proteins') database [Dodge et al. (1998) Nucleic Acids Res., 26, 313-315]. Whereas each HSSP entry lists all protein sequences related to a given 3D structure, PSSH is the 'inverse', with each entry listing all structures related to a given sequence. In addition, we introduce two other derived databases: HSSPchain, in which each entry lists all sequences related to a given PDB chain, and HSSPalign, in which each entry gives details of one sequence aligned onto one PDB chain. This re-organization makes it easier to navigate from sequence to structure, and to map sequence features onto 3D structures. Currently (September 2002), PSSH provides structural information for over 400 000 protein sequences, covering 48% of SWALL and 61% of SWISS-PROT sequences; HSSPchain provides sequence information for over 25 000 PDB chains, and HSSPalign gives over 14 million sequence-to-structure alignments. The databases can be accessed via SRS 3D, an extension to the SRS system, at http://srs3d.ebi.ac.uk/.

Citing Articles

Dark Proteome Database: Studies on Dark Proteins.

Perdigao N, Rosa A High Throughput. 2019; 8(2).

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The Dark Proteome Database.

Perdigao N, Rosa A, ODonoghue S BioData Min. 2017; 10:24.

PMID: 28736578 PMC: 5520327. DOI: 10.1186/s13040-017-0144-6.

Integrated visual analysis of protein structures, sequences, and feature data.

Stolte C, Sabir K, Heinrich J, Hammang C, Schafferhans A, ODonoghue S BMC Bioinformatics. 2015; 16 Suppl 11:S7.

PMID: 26329268 PMC: 4547178. DOI: 10.1186/1471-2105-16-S11-S7.

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.

Satagopam V, Theodoropoulou M, Stampolakis C, Pavlopoulos G, Papandreou N, Bagos P Database (Oxford). 2010; 2010:baq019.

PMID: 20689020 PMC: 2931634. DOI: 10.1093/database/baq019.

Visualization of macromolecular structures.

ODonoghue S, Goodsell D, Frangakis A, Jossinet F, Laskowski R, Nilges M Nat Methods. 2010; 7(3 Suppl):S42-55.

PMID: 20195256 PMC: 7097155. DOI: 10.1038/nmeth.1427.

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