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Protocols

HOMSTRAD specifications

Information


Unique identifier OMICS_00976
Name HOMSTRAD
Alternative names HOMologous STRucture Alignment Database, HOMSTRAD BETA
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Maintainer


This tool is not available anymore.

Additional information


http://www-cryst.bioc.cam.ac.uk/databases

Publication for HOMologous STRucture Alignment Database

HOMSTRAD citations

 (37)
library_books

A Generative Angular Model of Protein Structure Evolution

2017
Mol Biol Evol
PMCID: 5850488
PMID: 28453724
DOI: 10.1093/molbev/msx137

[…] c HMM approach, similar to , that assumes dependencies between evolutionary processes at neighboring aligned positions.Parameters of ETDBN were estimated using 1,200 homologous protein pairs from the HOMSTRAD database (). The resulting model provides a realistic prior distribution over proteins and protein structure evolution in comparison to previous stochastic models. Doing so enables biological […]

library_books

QuickProbs 2: Towards rapid construction of high quality alignments of large protein families

2017
Sci Rep
PMCID: 5282490
PMID: 28139687
DOI: 10.1038/srep41553

[…] zed FASTA format from Robert Edgar’s Webpage and consist of small and moderate sequence sets (up to tens of sequences in the majority of cases). The latter were constructed by enriching respectively, Homstrad and BAliBASE benchmarks, with full protein families from Pfam. Number of sequences in BaliFam sets is in the order of 1,000 while Homfam contains much larger families of more than 100,000 mem […]

library_books

Characterization of multiple sequence alignment errors using complete likelihood score and position shift map

2016
BMC Bioinformatics
PMCID: 4799563
PMID: 26992851
DOI: 10.1186/s12859-016-0945-5

[…] e identical sequence set. Traditional evaluations of the MSA accuracy and characterizations of MSA errors used some benchmark sets of reference MSAs, typically based on structural alignments, such as HOMSTRAD [], BAliBASE [] PREFAB [], SAD [], and SABmark []. An inevitable problem in principle with these benchmark sets is that nobody knows whether or not each reference MSA is indeed the true MSA t […]

call_split

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

2014
PLoS One
PMCID: 4242723
PMID: 25419655
DOI: 10.1371/journal.pone.0113811
call_split See protocol

[…] p modeling tests in framework structures from thermal ensembles.The fourth type of test set consists of loop targets in template-based models. The protein targets for this set were collected from the HOMSTRAD set . Template-based models for the protein targets were generated using MODELLER 9.6 with templates and multiple sequence alignments taken from the SALIGN benchmark study , (downloaded fro […]

library_books

Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models

2014
J Comput Aided Mol Des
PMCID: 3927061
PMID: 24442887
DOI: 10.1007/s10822-013-9704-0

[…] ent. A search carried out with FUGUE [], a server specialized in alignment able to recognise homologue proteins by comparing sequences and structures, identified three “families” as classified in the Homstrad database [] with a Z-score larger than 6.0, the threshold over which the server identifies homologous with 99 % of confidence. Their representative structures were the GluCl receptor 3RHW [], […]

library_books

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub domain architecture

2013
BMC Struct Biol
PMCID: 4016585
PMID: 24131821
DOI: 10.1186/1472-6807-13-20

[…] les are expected to correlate. A module inferred from this type of data indicates that a defined subset of the protein structure is evolving as a unit. The α-amylase catalytic domain dataset from the Homstrad database [] was used to assess clustering in an evolutionary perspective. The structures used, the sampling strategy, and the alignment method used are explained further in the Methods sectio […]


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HOMSTRAD institution(s)
Department of Biochemistry, University of Cambridge, Cambridge, UK
HOMSTRAD funding source(s)
Supported by a Wellcome Trust Research Career Development Fellowship.

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