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).
| Software | Location | Web Site |
| GoMiner | NCI, NIH | http://discover.nci.nih.gov/gominer/ |
| GoSurfer | Harvard Univ. | http://www.biostat.harvard.edu/complab/gosurfer/ |
| GenMAPP | UC San Francisco | http://www.genmapp.org |
| ArrayTrack | US Food and Drug Administration (FDA) | http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm | caGEDA | Univ. of Pittsburgh | http://bioinformatics.upmc.edu/GE2/GEDA.html | SAM | Stanford Univ. | http://www-stat.stanford.edu/~tibs/SAM/ | NUDGE | Univ. of Washington | http://www.bioconductor.org |
| Software | Location | Web Site |
| GEO | NCBI, NIH | http://www.ncbi.nlm.nih.gov/projects/geo/ |
| ArrayExpress | EMBL-EBI | http://www.ebi.ac.uk/arrayexpress/ |
| CIBEX | Nat. Inst. Genetics, Japan | http://cibex.nig.ac.jp |
| Standard Microarray Database (SMD) | Stanford Univ. | http://smd.stanford.edu/ |
| The Gene Expression Database (GXD) | The Jackson Lab. | http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml |
| Oncomine | Univ. of Michigan | http://www.oncomine.org |
Protein Function Prediction Tools
| Software | Type | Location | Web Site |
| BLAST | Homology search | NCBI, NIH | http://www.ncbi.nlm.nih.gov/BLASTselect protein-protein BLAST |
| FASTA | Homology search | Virginia Univ.Kyoto Univ. | http://fasta.bioch.virginia.eduhttp://fasta.genome.jp/ |
| PSI-BLAST | Homology search | NCBI, NIH | http://www.ncbi.nlm.nih.gov/BLASTselect PSI- and PHI-BLAST |
| Pfam | Protein family identification | Washington Univ. | http://pfam.wustl.edu |
| SMART | Conserved Motif search | EMBL | http://smart.embl-heidelberg.de |
| PROSITE | Functional Motif search | Swiss Inst. Bioinformatics | http://us.expasy.org/prositehttp://motif.genome.ad.jp |
| ELM | Functional motif search in eukaryotes | The ELM Consortium | http://elm.eu.org |
| STRING | Function prediction by comparative genomics | EMBL | http://string.embl.de |
| PSORT | Subcellular localization prediction | Human Genome Center, Tokyo Univ. | http://www.psort.org |
| PFP | Function prediction by mining PSI-BLAST result | Purdue Univ. | http://dragon.bio.purdue.edu/pfp |
Protein Structure Prediction Tools
| Software | Type | Location | Web Site |
| PSIPRED | 2ndary structure | Univ. College London | http://bioinf.cs.ucl.ac.uk/psipred/ |
| PORTER | 2ndary structure | Univ. College Dublin | http://distill.ucd.ie/porter/ |
| SAM-T02 | 2ndary structure | UC Santa Cruz | http://www.cse.ucsc.edu/research/compbio/HMM-apps/T02-query.html |
| SABLE | 2ndary str., solvent accesibility | Cincinnati Children's Hospital Med. Center | http://sable.cchmc.org/ |
| PredictProtein | 2ndary structure and others | Columbia Univ. | http://cubic.bioc.columbia.edu/predictprotein/ |
| COILS | Coiled-coil region | EMBnet, Switzerland | http://www.ch.embnet.org/software/COILS_form.html |
| GlobPlot | Disordered region | EMBL | http://globplot.embl.de/ |
| PONDR | Disordered region | Indiana Univ. | http://www.pondr.com/ |
| TMHMM | Transmembrane domain | Technical Univ. of Denmark | http://www.cbs.dtu.dk/services/TMHMM-2.0/ |
| HMMTOP | Transmembrane domain | Hungarian Academy of Sciences | http://www.enzim.hu/hmmtop/ |
| SWISS-MODEL | 3D structure; (Homology modeling) | Swiss Inst. of Bioinformatics | http://swissmodel.expasy.org |
| HHPred | 3D str.; (Homology modeling) | Max-Planck Inst. | http://protevo.eb.tuebingen.mpg.de/toolkit/index.php?view=hhpred |
| MODELLER | 3D str.; (Homology modeling) | UC San Francisco | http://salilab.org/modeller/ |
| FUGUE | 3D str., threading | Univ. of Cambridge | http://www-cryst.bioc.cam.ac.uk/~fugue/ |
| Phyre | 3D str., threading | Imperial College London | http://www.sbg.bio.ic.ac.uk/~phyre/ |
| SPARKS | 3D str., threading | SUNY Buffalo | http://phyyz4.med.buffalo.edu/hzhou/anonymous-fold-sparks2.html |
| Robetta | 3D str; ab initio | Univ. Washington | http://robetta.bakerlab.org/ |
Additional Structure Prediction Tools
| Tool/DB | Type | Location | Website |
| GOR IV | 2ndary structure | PBIL,Lyon, France | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html |
| PROF | 2ndary structure | University of Wales, Aberystwyth | http://www.aber.ac.uk/%7Ephiwww/prof/ |
| PSA | 2ndary structure & 3D str., threading | Boston University | http://bmerc-www.bu.edu/psa/#topics |
| Protinfo | protein 3D/2D str. and others | University of Washington, Seattle | |
| 3D-JIGSAW | 3D str.; (Homology modeling) | Cancer Research UK London Research Institute | http://www.bmm.icnet.uk/servers/3djigsaw/ |
| ESyPred3D | 3D str.; (Homology modeling) | The University of Namur, Belgium. | http://www.fundp.ac.be/urbm/bioinfo/esypred/ |
| GENO3D | 3D str.; (Homology modeling) | PBIL,Lyon, France | http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html |
| DSC1 | 3D str.; (Homology modeling) | San Diego Supercomputer Center (SDSC). | http://cl.sdsc.edu/hm.html |
| FoldClass | 3D str., threading | DKFZ,Heidelberg, Germany | http://genome.dkfz-heidelberg.de/cgi-bin/w2hdemo/nph-w2h.helpapp?foldclass |
| Fold Recognition | 3D str., threading | UCLA | http://www.doe-mbi.ucla.edu/Services/FOLD/ |
Protein Protein Interaction Databases & Database Tools
| DB/Software | Type | Location | Web Site |
| BIND | PPI, pathway | Mt. Sinai Hospital, Canada | http://bind.ca/ |
| DIP | PPI | UC Los Angeles | http://dip.doe-mbi.ucla.edu/ |
| MIPS | Mammalian PPIs | Munich Information Center for Protein Sequences | http://mips.gsf.de/proj/ppi/ |
| HPRD | Human protein references | Johns Hopkins Univ. | http://www.hprd.org/ |
| GRID | genetic and physical interactions of yeast, fry, worm | Mt. Sinai Hospital, Canada | http://biodata.mshri.on.ca/grid/ |
| IntAct | open source db systems & tools for PPI data | EBI | http://www.ebi.ac.uk/intact/ |
| Ospray | PPI visualization tool | Mt. Sinai Hospital, Canada | http://biodata.mshri.on.ca/osprey/ |
| Tool/DB | Type | Location | Website |
| Structure Prediction & Databases | Resources | San Diego Supercomputer Center (SDSC). | http://restools.sdsc.edu/biotools/biotools9.html |
| NIH Molecular Modeling Homepage | Resources | NIH,USA | http://cmm.info.nih.gov/modeling/ |
| Microarray Software Comparison | Links | The Chinese Univ. of Hong Kong, China | http://ihome.cuhk.edu.hk/~b400559/arraysoft_rpackages.html |
Maintained by Yifeng D. Yang, questions and comments to yang41@ purdue.edu
Last updated on Jan 6 2006.