3DBIONOTES: A unified, enriched and interactive view of macromolecular information

D Tabas-Madrid; J Segura; R Sanchez-Garcia; J Cuenca-Alba; C O S Sorzano; J M Carazo

doi:10.1016/j.jsb.2016.02.007

3DBIONOTES: A unified, enriched and interactive view of macromolecular information

J Struct Biol. 2016 May;194(2):231-4. doi: 10.1016/j.jsb.2016.02.007. Epub 2016 Feb 10.

Authors

D Tabas-Madrid¹, J Segura², R Sanchez-Garcia¹, J Cuenca-Alba¹, C O S Sorzano¹, J M Carazo¹

Affiliations

¹ GN7 of the Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain.
² GN7 of the Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain. Electronic address: jsegura@cnb.csic.es.

PMID: 26873783
DOI: 10.1016/j.jsb.2016.02.007

Abstract

With the advent of high throughput techniques like Next Generation Sequencing, the amount of biological information for genes and proteins is growing faster than ever. Structural information is also rapidly growing, especially in the cryo Electron Microscopy area. However, in many cases, the proteomic and genomic data are spread in multiple databases and with no simple connection to structural information. In this work we present a new web platform that integrates EMDB/PDB structures and UniProt sequences with different sources of protein annotations. The application provides an interactive interface linking sequence and structure, including EM maps, presenting the different sources of information at sequence and structural level. The web application is available at http://3dbionotes.cnb.csic.es.

Keywords: Database integration; Protein annotations; Protein sequence; Protein structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenomatous Polyposis Coli Protein / chemistry
Adenomatous Polyposis Coli Protein / genetics
Adenomatous Polyposis Coli Protein / metabolism
Amino Acid Sequence
Antigens, CD
Base Sequence
Cadherins / chemistry
Cadherins / genetics
Cadherins / metabolism
Cell Cycle Proteins / chemistry
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism
Databases, Protein
F-Box Proteins / chemistry
F-Box Proteins / genetics
F-Box Proteins / metabolism
Gene Expression
Humans
Internet
Models, Molecular
Protein Conformation
Proteomics / statistics & numerical data*
Proto-Oncogene Proteins p21(ras) / chemistry
Proto-Oncogene Proteins p21(ras) / genetics
Proto-Oncogene Proteins p21(ras) / metabolism
Software*
Structure-Activity Relationship

Substances

APC protein, human
Adenomatous Polyposis Coli Protein
Antigens, CD
CDH1 protein, human
Cadherins
Cell Cycle Proteins
F-Box Proteins
FBXO5 protein, human
HRAS protein, human
Proto-Oncogene Proteins p21(ras)