User:Wayne Decatur/Homology Modeling: Difference between revisions

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**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://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-Tasser] - "is an Internet service for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. The server is in active development with the goal to provide the most accurate structural and function predictions using state-of-the-art algorithms."

*[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-Tasser]:

** '''Employs more of comparative protein modelling based on protein threading and not a homology model from what I gather '''

**"I-Tasser is an Internet service for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. The server is in active development with the goal to provide the most accurate structural and function predictions using state-of-the-art algorithms."

*[http://swift.cmbi.ru.nl/teach/courses/index.html Course on Homology Modeling]

*[http://www.udel.edu/chem/bahnson/chem645/Part-I-645homology_F08.html Class on Homology Modeling]

@@ Line 13: / Line 13: @@
 **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://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-Tasser] - "is an Internet service for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. The server is in active development with the goal to provide the most accurate structural and function predictions using state-of-the-art algorithms."
+*[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-Tasser]:
+** '''Employs more of comparative protein modelling based on protein threading and not a homology model from what I gather '''
+**"I-Tasser is an Internet service for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. The server is in active development with the goal to provide the most accurate structural and function predictions using state-of-the-art algorithms."
 *[http://swift.cmbi.ru.nl/teach/courses/index.html Course on Homology Modeling]
 *[http://www.udel.edu/chem/bahnson/chem645/Part-I-645homology_F08.html Class on Homology Modeling]