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HSSP specifications

Information


Unique identifier OMICS_30165
Name HSSP
Alternative name Homology-derived Secondary Structure of Proteins
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Liisa Holm

Publications for Homology-derived Secondary Structure of Proteins

HSSP citations

 (40)
library_books

Mutation Structure Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach

2017
Int J Mol Sci
PMCID: 5297772
PMID: 28085066
DOI: 10.3390/ijms18010139

[…] ral features of mutations on native protein molecule, Project HOPE uses 3D structures of the proteins that are available in UniProt database. The web server utilizes FASTA, BLAST, UniProt, PDB, DSSP, HSSP, YASARA, ClustalW, and DAS server to make its prediction on protein structure. The HOPE server predicts structural variation between native protein and the variant models and can also build homol […]

library_books

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders

2017
Hum Mol Genet
PMCID: 5409128
PMID: 28053047
DOI: 10.1093/hmg/ddw409

[…] chain sterically interferes with the backbone of the preceding turn and the backbone nitrogen is unable to participate in backbone hydrogen bonds that stabilize α-helices. Moreover, according to the HSSP alignments, the leucine at this position is highly structurally conserved (99%); the only other amino acid observed at this position is the similar valine. Leu207 is highly buried – its accessibl […]

library_books

Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate algal symbiosis

2017
eLife
PMCID: 5413350
PMID: 28462779
DOI: 10.7554/eLife.22054.049

[…] and O. amblystomatis transcripts was accomplished by BLASTX of transcripts against the UniProt-SWISSProt curated database (). BLASTX results were filtered by ‘homology-derived structure of proteins’ (HSSP) score () such that annotations were retained for hits with an HSSP_DIST score greater than 5 (). UniProt ID annotations were assigned based on the maximum HSSP score for each gene. This led to 1 […]

library_books

The Path to Enlightenment: Making Sense of Genomic and Proteomic Information

2016
PMCID: 5172447
PMID: 15629052
DOI: 10.1016/S1672-0229(04)02018-2

[…] tion about the close relatives of any particular protein .3Dee contains structural domain definitions for all protein chains in the PDB that have 20 or more residues and are not theoretical models , .HSSP is a database of Homology-derived Secondary Structures of Proteins and contains information about aligned sequences, secondary structure, sequence variability and sequence profile of known protei […]

library_books

Computational prediction shines light on type III secretion origins

2016
Sci Rep
PMCID: 5054392
PMID: 27713481
DOI: 10.1038/srep34516

[…] or ‘fragment’. We reduced sequence redundancy independently in each set using UniqueProt, ascertaining that no pair of proteins in one set had alignment length of less than 35 residues or a positive HSSP-value (HVAL ≥ 0). After redundancy reduction our sequence-unique sets contained 115 type III effector proteins from 43 different bacterial species and 3,460 non-effector proteins (of which 37% we […]

library_books

A novel secondary structure based on fused five membered rings motif

2016
Sci Rep
PMCID: 4980606
PMID: 27511362
DOI: 10.1038/srep31483

[…] topi in terms of entropy. Shanon entropy at each position in the motif was calculated by considering multiple sequence alignment of all possible homologs of the protein (sequence identity ≥60%) using HSSP (homology-derived secondary structures of proteins) database. A residue in topi was considered as conserved if its entropy was less than the average entropy of the protein chain.We used the stati […]

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HSSP institution(s)
European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge, UK; Whitehead Institute, MIT Genome Center, Cambridge, MA, USA

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