LibGuides: Biomedical Big Data Resource Center: Databases & Tools

Databases & Tools

Aquaria
Tool for looking at similar protein structure to a query.
Cn3D macromolecular structure viewer
Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

Database of Interacting Proteins (DIP)
Catalogs experimentally determined interactions between proteins.
STRING
A database of known and predicted protein-protein interactions.
HumanNet
A probabilistic functional gene network of 18,714 validated protein-encoding genes of Homo sapiens (by NCBI March 2007), constructed by a modified Bayesian integration of 21 types of 'omics' data from multiple organisms.

GREMLIN (Baker Lab)
GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family.
TCS
The Bayesian algorithm expicitly models the amino acid composition of interacting kinase / regulator pairs to predict interaction specificity of orphan kinases and regulators across all sequenced bacterial genomes.

Rate4Site
A program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA).
PAGAN-MSA (alignment of sequence graphs)
PRANK - multiple sequence alignment
GUIDANCE server
Contains implementations of many of the above algorithms
NCBI Splign
Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments.

PRIDE Archive
The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.