User:Wayne Decatur/Homology Modeling: Difference between revisions
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*[http://swissmodel.expasy.org/ SwissModel] | *[http://swissmodel.expasy.org/ SwissModel] | ||
*[http://spdbv.vital-it.ch/ Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at...] Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel. | *[http://spdbv.vital-it.ch/ Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at...] Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel. | ||
*[http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] also allows users to calculate comparative models on demand. | |||
*[http://salilab.org/modeller/ Modeller] | |||
*[http://www.ncbi.nlm.nih.gov/pubmed/17640066 The Homology Modeling Automatically (HOMA) web site] | |||
*[http://www.yasara.org/ YASARA] - Yet Another Scientific Artificial Reality Application) features a complete homology modeling module that fully automatically takes all the steps from an amino acid sequence to a refined high-resolution model using a CASP approved protocol. | |||
*[http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html SAM-T08: HMM-nased structure prediction.] | |||
*Interesting note on the site page "This server was tested as SAM_T08_server in the CASP8 experiment. Preliminary results indicate that it is a good primary server, but that metaservers combining results from several primary servers are likely to produce somewhat better results." | |||
*As per the site-"This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed. Look carefully at the E-values for the best hits, as full 3D models are constructed even when the E-values are high (and the resulting models are not then not trustworthy)." | |||
*[http://www.yasara.org/homologymodeling.htm Yasara to homology model] | |||
*[http://spdbv.vital-it.ch/TheMolecularLevel/Matics/index.html Gale Rhodes Homology modeling tutorial using Swiss PDB Viewer (DeepView)] | |||
*[http://www.biochem.vt.edu/modeling/homology.html David Bevan's homology modeling page] | *[http://www.biochem.vt.edu/modeling/homology.html David Bevan's homology modeling page] | ||
*[http://swift.cmbi.ru.nl/teach/courses/index.html Course on Homology Modeling] | *[http://swift.cmbi.ru.nl/teach/courses/index.html Course on Homology Modeling] | ||
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*[http://biskit.pasteur.fr/use/workflows/homology-modelling Biskit that uses python for homology modeling] | *[http://biskit.pasteur.fr/use/workflows/homology-modelling Biskit that uses python for homology modeling] | ||
*[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07070.html note on Pymol for homology modeling] | *[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07070.html note on Pymol for homology modeling] | ||