| | Typea | URLb |
|---|
DATABASES |
| CATH | S | http://www.biochem.ucl.ac.uk/bsm/cath/ |
| DBAli | S | http://www.salilab.org/DBAli/ |
| GenBank | S | http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html |
| GeneCensus | S | http://bioinfo.mbb.yale.edu/genome |
| MODBASE | S | http://salilab.org/modbase/ |
| MSD | S | http://www.rcsb.org/databases.html |
| NCBI | S | http://www.ncbi.nlm.nih.gov/ |
| PDB | S | http://www.rcsb.org/pdb/ |
| PSI | S | http://www.nigms.nih.gov/psi/ |
| Sacch3D | S | http://genome-www.stanford.edu/Sacch3D/ |
| SCOP | S | http://scop.mrc-lmb.cam.ac.uk/scop/ |
| TIGR | S | http://www.tigr.org/tdb/mdb/mdbcomplete.html |
| UniProtKB | S | http://www.uniprot.org/ |
FOLD ASSIGNMENT |
| 123D | S | http://123d.ncifcrf.gov/ |
| 3D-PSSM | S | http://www.sbg.bio.ic.ac.uk/~3dpssm/ |
| BIOINBGU | S | http://www.cs.bgu.ac.il/~bioinbgu/ |
| BLAST | S | http://www.ncbi.nlm.nih.gov/BLAST/ |
| DALI | S | http://www2.ebi.ac.uk/dali/ |
| FASS | S | http://bioinformatics.burnham-inst.org/FFAS/index.html |
| FastA | S | http://www.ebi.ac.uk/fasta3/ |
| FRSVR | S | http://fold.doe-mbi.ucla.edu/ |
| FUGUE | S | http://www-cryst.bioc.cam.ac.uk/~fugue/ |
| LOOPP | S | http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm |
| PDB-BLast/FASS | S | http://bioinformatics.ljcrf.edu/pdb_blast/ |
| PHD, TOPITS | S | http://www.predictprotein.org/ |
| PROFIT | P | http://www.came.sbg.ac.at/ |
| SAM-T99/T98 | S | http://www.cse.ucsc.edu/research/compbio/HMM-apps/ |
| THREADER | S | http://bioinf.cs.ucl.ac.uk/threader/ |
| UCLA-DOE FRSVR | S | http://fold.doe-mbi.ucla.edu/ |
SEQUENCE ALIGNMENT |
| BCM SERVER | S | http://searchlauncher.bcm.tmc.edu |
| BLAST2 | S | http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi |
| BLOCK MAKER | S | http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html |
| CLUSTALW | S | http://www2.ebi.ac.uk/clustalw/ |
| FASTA3 | S | http://www2.ebi.ac.uk/fasta3/ |
| Gerstein Group | S | http://bioinfo.mbb.yale.edu/Align/ |
| MULTALIN | S | http://prodes.toulouse.inra.fr/multalin/multalin.html |
MODELING |
| 3D-JIGSAW | S | http://www.bmm.icnet.uk/servers/3djigsaw/ |
| CPH-Models | S | http://www.cbs.dtu.dk/services/CPHmodels/ |
| COMPOSER | P | http://www-cryst.bioc.cam.ac.uk/ |
| CONGEN | P | http://www.congenomics.com/congen/congen.html |
| TIGERFAMS | S | http://www.tigr.org/TIGRFAMs/index.shtml |
| ICM (a) | P | http://www.molsoft.com/ |
| InsightII (b) | P | http://www.accelrys.com/ |
| MODELLER | P | http://salilab.org/modeller/modeller.html |
| ModWeb | S | http://salilab.org/modweb |
| QUANTA (b) | P | http://www.accelrys.com/ |
| SYBYL (c) | P | http://www.tripos.com/ |
| SCWRL | P | http://dunbrack.fccc.edu/SCWRL3.php |
| SDSC1 | S | http://cl.sdsc.edu/hm.html |
| SWISS-MODEL | S | http://www.expasy.ch/swissmod/SWISS-MODEL.html |
| WHAT IF | P | http://www.cmbi.kun.nl/whatif/ |
MODEL EVALUATION |
| ANOLEA | S | http://protein.bio.puc.cl/cardex/servers/index.html |
| BIOTECHd | S | http://biotech.embl-ebi.ac.uk:8400/ |
| CAFASP | S | http://bioinfo.pl/cafasp/ |
| ERRAT | S | http://www.doe-mbi.ucla.edu/Services/ERRATv2/ |
| EVA | S | http://cubic.bioc.columbia.edu/eva/ |
| LiveBench | S | http://bioinfo.pl/LiveBench/ |
| PROCHECK | P | http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html |
| ProsaIIe | P | http://www.came.sbg.ac.at/ |
| PROVE | S | http://www.ucmb.ulb.ac.be/UCMB/PROVE |
| VERIFY3D | S | http://www.doe-mbi.ucla.edu/Services/Verify_3D/ |
| WHATCHECK | P | http://www.sander.embl-heidelberg.de/whatcheck/ |
COMPARATIVE AND DOCKING MODEL ASSESSMENT |
| CLUSPRO | S | http://nrc.bu.edu/cluster/cluspro_v1.cgi |
| COMBINATORIAL_EXTENSION | S | http://cl.sdsc.edu/ce.html |
| DFIRE | S | http://sparks.informatics.iupui.edu/hzhou/dfire.html |
| FASTCONTACT | S | http://structure.pitt.edu/servers/fastcontact/ |
| FIBERDOCK | S | http://bioinfo3d.cs.tau.ac.il/FiberDock/ |
| METAMQAPII | S | https://genesilico.pl/toolkit/unimod?method=MetaMQAPII |
| MODFOLD | S | http://www.reading.ac.uk/bioinf/ModFOLD/ModFOLD_form_2_0.html |
| GENTHREADER | S | http://bioinf4.cs.ucl.ac.uk:3000/psipred/ |
| PCONS | S | http://pcons.net/ |
| PROQ | S | http://www.sbc.su.se/~bjornw/ProQ/ProQ.html |
| PROSA-WEB | S | https://prosa.services.came.sbg.ac.at/prosa.php |
| QMEAN | S | http://swissmodel.expasy.org/qmean/cgi/index.cgi |
| RAMPAGE | S | http://mordred.bioc.cam.ac.uk/~rapper/rampage.php |
| TASSER | S | http://zhanglab.ccmb.med.umich.edu/I-TASSER/ |
| TM-SCORE | S | http://zhanglab.ccmb.med.umich.edu/TM-score/ |
| VERIFY3D | S | http://nihserver.mbi.ucla.edu/Verify_3D/ |
OTHERS... |
| BioInfo | S | http://BioInfo.PL/meta/ |
| Bork Group | S | http://dove.embl-heidelberg.de/3D/ |
| CASP | S | http://predictioncenter.llnl.gov/ |
| GeneQuiz II | S | http://columba.ebi.ac.uk:8765/ext-genequiz/ |
| Gerstein Group | S | http://bioinfo.mbb.yale.edu/genome/ |
| META-PP | S | http://cubic.bioc.columbia.edu/pp/doc/meta_intro.html |
| PEDANT | S | http://pedant.gsf.de/ |
| SearchLauncher | S | http://searchlauncher.bcm.tmc.edu/ |
| WorkBench | S | http://workbench.sdsc.edu/ |
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