User:Wayne Decatur/Homology Modeling: Difference between revisions
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*[http://www.ncbi.nlm.nih.gov/pubmed/17640066 The Homology Modeling Automatically (HOMA) web site] | *[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://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://www.yasara.org/homologymodeling.htm Yasara to homology model] | |||
*[http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html SAM-T08: HMM-based structure prediction.] | *[http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html SAM-T08: HMM-based 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." | **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)." | **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.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] | ||
Revision as of 22:11, 12 November 2010
- Homology modeling page at Proteopedia
- Eric Martz's Homology modeling of DnaC
- SwissModel
- 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.
- Gale Rhodes Homology modeling tutorial using Swiss PDB Viewer (DeepView)
- ModBase: Database of Comparative Protein Structure Models also allows users to calculate comparative models on demand.
- Modeller is associated with ModBase
- The Homology Modeling Automatically (HOMA) web site
- 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.
- SAM-T08: HMM-based 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)."
- David Bevan's homology modeling page
- Course on Homology Modeling
- Class on Homology Modeling
- Biskit that uses python for homology modeling
- note on Pymol for homology modeling
See AlsoSee Also
- Homology model
- Molecular modeling and visualization software
- List of software for molecular mechanics modeling at Wikipeida although thoroughness and how current it is are subject to question by the inclusion of RasMol which is simply a viewer with no modeling abilities that has been supplanted by better viewers such as Chime and Jmol not included on the list.