Tag: Structural Information

TAGOPSIN 1.3 – Collating Taxa-specific Gene and Protein Functional and Structural Information

TAGOPSIN 1.3

:: DESCRIPTION

TAGOPSIN (TAxonomy, Gene, Ontology, Protein, Structure INtegrated) retrieves select data from NCBI Taxonomy, NCBI Nucleotide, UniProtKB, Gene Ontology, Pfam, EBI SIFTS and RCSB PDB, and assembles them in the database management system PostgreSQL. TAGOPSIN is an organism-centred data warehousing tool that works with prokaryotic and eukaryotic organisms as well as viruses.

::DEVELOPER

TAGOPSIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • PostgreSQL

:: DOWNLOAD

TAGOPSIN

:: MORE INFORMATION

Citation

Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y.
TAGOPSIN: collating taxa-specific gene and protein functional and structural information.
BMC Bioinformatics. 2021 Oct 23;22(1):517. doi: 10.1186/s12859-021-04429-5. PMID: 34688246; PMCID: PMC8541804.

NGlycPred – N-linked Glycosylation Prediction Server Incorporating Structural Information and Patterns

NGlycPred

:: DESCRIPTION

NGlycPred predicts the glycan occupancy of N-X-T/S sequons of eukaryotic proteins.

::DEVELOPER

NGlycPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2249-55. doi: 10.1093/bioinformatics/bts426. Epub 2012 Jul 10.
Computational prediction of N-linked glycosylation incorporating structural properties and patterns.
Chuang GY1, Boyington JC, Joyce MG, Zhu J, Nabel GJ, Kwong PD, Georgiev I.

BALL-SNP – Combining Genetic and Structural Information to Identify Candidate Non-synonymous SNPs

BALL-SNP

:: DESCRIPTION

BALL-SNPgp is the extension of the proof-of-concept tool BALL-SNP, a software tool based on the Biochemical Algorithms Library (BALL), a molecular modeling framework, providing robust and sophisticated algorithms on structural bioinformatics. BALL-SNPgp enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BALL

:: DOWNLOAD

 BALL-SNPgp

:: MORE INFORMATION

Citation:

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.
Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.
Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y.

PrePPI – Predicting Protein-Protein Interactions by Combining Structural and non-Structural Information

PrePPI

:: DESCRIPTION

PrePPI is a database of predicted and experimentally determined protein-protein interactions (PPI) for yeast and human. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information.

::DEVELOPER

Barry Honig’s group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrePPI: a structure-informed database of protein-protein interactions.
Zhang QC, Petrey D, Garzón JI, Deng L, Honig B.
Nucleic Acids Res. 2013 Jan;41(Database issue):D828-33. doi: 10.1093/nar/gks1231.