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タンパク質構造予測ソフトウェア [2013/06/09 09:08] (現在)
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 +======タンパク質構造予測ソフトウェア======
 +=====Wikipedia=====
 +  * Wikipedia - [[wp>​Protein_structure_prediction_software|Protein structure prediction software]](英語ページ)
 +
 +This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, and secondary structure prediction.
 +
 +**Homology modeling**
 +^  NAME  ^  Method ​ ^  Description ​ ^  Link  ^
 +|  MODELLER ​ |  Satisfaction of spatial restraints ​ |  Standalone program\\ in [[Python (programming language)|Python]] ​ | [[http://​salilab.org/​modeller/​|download]]||
 +|  SWISS-MODEL ​ |  Local similarity/​fragment assembly ​ |  Automated webserver\\ (based on ProModII) ​ |  [[http://​swissmodel.expasy.org/​|server]] ​ |
 +|  3D-JIGSAW ​ |  Fragment assembly ​ |  Automated webserver ​ |   ​[[http://​bmm.cancerresearchuk.org/​~3djigsaw/​|server]] ​ |
 +|  Geno3D ​ |  Satisfaction of spatial restraints ​ |  Automated webserver ​ |  [[http://​geno3d-pbil.ibcp.fr/​|server]] ​ |
 +|  CPHModel ​ |  Fragment assembly ​ |  Automated webserver ​ |  [[http://​www.cbs.dtu.dk/​services/​CPHmodels/​|server]] ​ |
 +|  GeneSilico ​ |  Consensus template search/​fragment assembly ​ |  Webserver ​ |  [[http://​www.genesilico.pl/​meta/​|server]] ​ |
 +|  WHAT IF  | Position specific rotamers ​ |  Webserver ​ |  [[http://​swift.cmbi.kun.nl/​WIWWWI/​|server]] ​ |
 +|  TIP-STRUCTFAST ​ |  Automated Comparative Modeling ​ |  Webserver and  [[http://​www.eidogen-sertanty.com/​products_tip_content.html|knowledgebase]] ​ |  [[https://​tip.eidogen-sertanty.com/​Login.po|server]] ​ |
 +|  CABS  |  Reduced modeling tool  |  Downloadable program ​ |  [[http://​www.biocomp.chem.uw.edu.pl/​services.php|download]] ​ |
 +
 +**Threading/​fold recognition**
 +^  NAME  ^  Method ​ ^  Description ​ ^  Link  ^
 +|  3D-PSSM ​ |  3D-1D sequence profiling ​ |  Webserver ​ | [[http://​www.sbg.bio.ic.ac.uk/​~3dpssm/​|server]] ​ |
 +|  Superfamily ​ |  Hidden Markov modeling ​ |  Webserver/​standalone ​ |  [[http://​supfam.mrc-lmb.cam.ac.uk/​SUPERFAMILY/​|main page]] ​ |
 +|  PSI-BLAST ​ |  Iterative sequence alignment for fold identification ​ |  Webserver ​ |   ​[[http://​www.ncbi.nlm.nih.gov/​blast/​|main page]] ​ |
 +|  Bioingbu ​ |  Evolutionary information recognition ​ |  Webserver ​ |  [[http://​www.cs.bgu.ac.il/​%7Ebioinbgu/​|server]] ​ |
 +|  PSIPRED/​GenTHREADER ​ |  Sequence profiling ​ |  Webserver ​ |  [[http://​bioinf.cs.ucl.ac.uk/​psipred/​|main page]] ​ |
 +|  LOOPP  |  Multiple methods ​ |  Webserver ​ |  [[http://​cbsuapps.tc.cornell.edu/​loopp.aspx|server]] ​ |
 +
 +**//Ab initio// structure prediction**
 +^  NAME  ^  Method ​ ^  Description ​ ^  Link  ^
 +|  ROSETTA/​ROBETTA ​ |  Fragment assembly without template ​ |  Webserver ​ |  [[http://​robetta.bakerlab.org/​|server]] ​ |
 +|  Rosetta@Home ​ |  Distributed-computing implementation of Rosetta algorithm ​ |   ​Downloadable program ​ |  [[http://​boinc.bakerlab.org/​rosetta/​|main page]] ​ |
 +|  CABS  |  Reduced modeling tool  |  Downloadable program ​ |  [[http://​www.biocomp.chem.uw.edu.pl/​services.php|download]] ​ |
 +
 +**Secondary structure prediction**
 +^  NAME  ^  Method ​ ^  Description ​ ^  Link  ^
 +|  GOR  |  Information theory/​Bayesian inference ​ |  Many implementations ​ |  [[http://​abs.cit.nih.gov/​gor/​|Basic GOR]]\\ [[http://​gor.bb.iastate.edu/​|GOR V]]  |
 +|  Jpred  |  Neural network assignment ​ |  Webserver ​ |  [[http://​www.compbio.dundee.ac.uk/​~www-jpred/​|server]] ​ |
 +|  PredictProtein ​ | Profile-based neural network ​ |  Webserver ​ |  [[http://​cubic.bioc.columbia.edu/​predictprotein/​|server]] ​ |
 +|  Meta-PP ​ |  Consensus prediction of other servers ​ |  Webserver ​ |   ​[[http://​cubic.bioc.columbia.edu/​predictprotein/​doc/​meta_intro.html|main page]] ​ |
 +|  PREDATOR ​ |  Knowledge-based database comparison ​ |  Webserver ​ |  [[http://​bioweb.pasteur.fr/​seqanal/​interfaces/​predator-simple.html|server]] ​ |
 +
 +Jpred compares the sequence of the query and the sequences found in the databases. Jpred uses a computer algorithm to allow for gaps, which represent insertions and deletions. This program identifies proteins that are homologous to the query sequence. Jpred also identifies if any homologous proteins have determined 3D structures.
 +
 +======リンク======
 +
 +  *[[タンパク質構造予測]]
 +
 +
 +{{tag>​タンパク質 立体構造}}