TY - JOUR
T1 - MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.
AU - Kosinski, Jan
AU - Barbato, Alessandro
AU - Tramontano, Anna
N1 - KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-012-43
Acknowledgements: KAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), Fondazione Roma, FIRB Italbionet and RBIN06E9Z8_005, and European Molecular Biology Organization (EMBO) Long-Term Fellowship to J.K.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.
PY - 2013/2/8
Y1 - 2013/2/8
N2 - SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
AB - SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UR - http://hdl.handle.net/10754/596803
UR - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt062
UR - http://www.scopus.com/inward/record.url?scp=84875627549&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btt062
DO - 10.1093/bioinformatics/btt062
M3 - Article
C2 - 23396123
SN - 1367-4803
VL - 29
SP - 953
EP - 954
JO - Bioinformatics
JF - Bioinformatics
IS - 7
ER -