Bioinformatics Resources for Microarray data analysis, Protein function/structure prediction, and Protein-protein interaction databases

Supplemental Materials for the paper "Bioinformatics resources for cancer research with an emphasis on protein function and structure prediction tools" by Daisuke Kihara, Yifeng David Yang and Troy Hawkins, Cancer Informatics, 2:25-35, (2006).

Microarray Analysis Software
Microarray Data Repositories
Protein Function Prediction Tools
Protein Structure Prediction Tools
Additional Structure Prediction Tools
Protein Protein Interaction Databases & Database Tools
Other bioinformatics links

Microarray Analysis Software

Software Location Web Site
GoMiner NCI, NIH
GoSurfer Harvard Univ.
GenMAPP UC San Francisco
ArrayTrack US Food and Drug Administration (FDA)
caGEDA Univ. of Pittsburgh
SAM Stanford Univ.
NUDGE Univ. of Washington


Microarray Data Repositories

Software Location Web Site
ArrayExpress EMBL-EBI
CIBEX Nat. Inst. Genetics, Japan
Standard Microarray Database (SMD) Stanford Univ.

The Gene Expression Database (GXD) The Jackson Lab.
Oncomine Univ. of Michigan


Protein Function Prediction Tools

Software Type Location Web Site
BLAST Homology search NCBI, NIH

select protein-protein BLAST
FASTA Homology search Virginia Univ.

Kyoto Univ.
PSI-BLAST Homology search NCBI, NIH

select PSI- and PHI-BLAST
Pfam Protein family identification Washington Univ.
SMART Conserved Motif search EMBL
PROSITE Functional Motif search Swiss Inst. Bioinformatics
ELM Functional motif search in eukaryotes The ELM Consortium
STRING Function prediction by comparative genomics EMBL
PSORT Subcellular localization prediction Human Genome Center, Tokyo Univ.
PFP Function prediction by mining  PSI-BLAST result Purdue Univ.


Protein Structure Prediction Tools

Software Type Location Web Site
PSIPRED 2ndary structure Univ. College London
PORTER 2ndary structure Univ. College Dublin
SAM-T02 2ndary structure UC Santa Cruz
SABLE 2ndary str., solvent accesibility Cincinnati Children's Hospital Med. Center
PredictProtein 2ndary structure and others Columbia Univ.
COILS Coiled-coil region EMBnet, Switzerland
GlobPlot Disordered region EMBL
PONDR Disordered region Indiana Univ.
TMHMM Transmembrane domain Technical Univ. of Denmark
HMMTOP Transmembrane domain Hungarian Academy of Sciences

SWISS-MODEL 3D structure; (Homology modeling) Swiss Inst. of Bioinformatics

HHPred 3D str.; (Homology modeling) Max-Planck Inst.

MODELLER 3D str.; (Homology modeling) UC San Francisco

FUGUE 3D str., threading Univ. of Cambridge

Phyre 3D str., threading Imperial College London

SPARKS 3D str., threading SUNY Buffalo
Robetta 3D str; ab initio Univ. Washington


Additional Structure Prediction Tools

Tool/DB Type Location Website
GOR IV 2ndary structure PBIL,Lyon, France
PROF 2ndary structure University of Wales, Aberystwyth
PSA 2ndary structure & 3D str., threading Boston University
Protinfo protein 3D/2D str. and others University of Washington, Seattle

3D-JIGSAW 3D str.; (Homology modeling) Cancer Research UK London Research Institute
ESyPred3D 3D str.; (Homology modeling) The University of Namur, Belgium.
GENO3D 3D str.; (Homology modeling) PBIL,Lyon, France
DSC1 3D str.; (Homology modeling) San Diego Supercomputer Center (SDSC).
FoldClass 3D str., threading DKFZ,Heidelberg, Germany
Fold Recognition 3D str., threading UCLA


Protein Protein Interaction Databases & Database Tools

DB/Software Type Location Web Site
BIND PPI, pathway Mt. Sinai Hospital, Canada

DIP PPI UC Los Angeles
MIPS Mammalian PPIs Munich Information Center for Protein Sequences

HPRD Human protein references Johns Hopkins Univ.

GRID genetic and physical interactions of yeast, fry, worm Mt. Sinai Hospital, Canada

IntAct open source db systems & tools for PPI data EBI

Ospray PPI visualization tool Mt. Sinai Hospital, Canada


Other bioinformatics links

Tool/DB Type Location Website
Structure Prediction & Databases Resources San Diego Supercomputer Center (SDSC).
NIH Molecular Modeling Homepage Resources NIH,USA
Microarray Software Comparison Links The Chinese Univ. of Hong Kong, China


Maintained by Yifeng D. Yang, questions and comments to yang41@
Last updated on Jan 6 2006.