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HOMCOS specifications

Information


Unique identifier OMICS_13637
Name HOMCOS
Alternative name HOMology modeling of COmplex Structure
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Takeshi Kawabata

Publications for HOMology modeling of COmplex Structure

HOMCOS citations

 (11)
library_books

Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi modal interaction ensemble to an auto inhibitory state

2018
Nucleic Acids Res
PMCID: 5861456
PMID: 29309620
DOI: 10.1093/nar/gkx1297

[…] motif forms salt-bridges with the RXXR motif in the PDB (), numerous interacting pairs of α- and 310-helices have been reported. Some examples are shown in , and the details of the analysis using the HOMCOS database () are described in .In addition, the importance of the two aromatic residues adjacent to the pSer for the effects of the phosphorylation suggested by the experiments (See Y283A and F2 […]

library_books

A novel rare variant R292H in RTN4R affects growth cone formation and possibly contributes to schizophrenia susceptibility

2017
PMCID: 5611737
PMID: 28892071
DOI: 10.1038/tp.2017.170

[…] monomeric 3D structures (PDBIDs: 1p8t and 4oqt, respectively) on the template 3D structure of the human SLITRK1 and PTPRD complex (PDBID: 4rca). The template structure was found with the help of the HOMCOS server by the condition that the 292-nd site of RTN4R became an interface for other proteins. The sequence of the SLITRK1 protein is similar to that of RTN4R, with 33.5% sequence identity, and […]

library_books

Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders

2017
PMCID: 5611740
PMID: 28763059
DOI: 10.1038/tp.2017.173

[…] found by the BLAST program in the 3D structural database. The sequence identity between CX3CR1 and CCR2 isoform B is about 46%. The template structure and the BLAST alignment were downloaded from the HOMCOS server, and manually modified to remove the region of T4 lysozome in the structure. The program MODELLER 9.16 was used for the modeling. Bound structures of membrane, fractalkine and heterotrim […]

library_books

Multimer recognition and secretion by the non classical secretion pathway in Bacillus subtilis

2017
Sci Rep
PMCID: 5343618
PMID: 28276482
DOI: 10.1038/srep44023

[…] has not yet been identified, a predicted tertiary structure of homotetramer RDPE was generated based on the template of D-Psicose 3-epimerase from Clostridium cellulolyticum H10 (PDB ID: 3VNK) by the HOMCOS server. The Try-118 (in the HD2 domain) and Ile-191(in the HD4 domain) residues from each of the two RDPE dimers (A-B, C-D) were found in close proximity (), supporting the notion that the two […]

library_books

Precursor N cadherin mediates glial cell line derived neurotrophic factor promoted human malignant glioma

2017
Oncotarget
PMCID: 5421898
PMID: 28212546
DOI: 10.18632/oncotarget.15302

[…] The homology model of a GDNF dimer based on the crystal structure of Rattus norvegicus GNDF-GFRα1 (PDB ID: 3fub, Chain A and D, x-ray diffraction) was constructed using the HOMCOS (http://homcos.pdbj.org/). Because the sequences of human and Rattus norvegicus GDNF mRNA (NM_000514.4 and NC_005101.4, respectively) are 100% consistent, the homolog crystal structure of GDNF […]

library_books

In Vitro Tolerance of Drug Naive Staphylococcus aureus Strain FDA209P to Vancomycin

2017
Antimicrob Agents Chemother
PMCID: 5278750
PMID: 27855063
DOI: 10.1128/AAC.01154-16

[…] ard and reverse primers specific for each target locus. Structural and evolutionary information for proteins affected by nonsynonymous SNPs was searched for using the protein database HOMOCOS (http://homcos.pdbj.org/?LANG=ja). […]

Citations

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HOMCOS institution(s)
Institute for Protein Research, Osaka University, Suita, Japan
HOMCOS funding source(s)
This work is supported by the Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from Japan Agency for Medical Research and Development (AMED).

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