User:Wayne Decatur/Homology Modeling

From Proteopedia

Current revision

• Protein Structure
  • 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)
  • HHpred - Homology detection & structure prediction by HMM-HMM comparison - Because homology modeling relies on identifying homologous sequences with known structure to be used as template and this serve is more sensitive at finding remote homologs, this server has been shown to perform well at template-based structure prediction (see CASP9 results).
    • 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.
    • Yasara to homology model
  • 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)."
    • MAY NOT BE WORKING AFTER FAILED IN 2014?
  • David Bevan's homology modeling page
  • 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 insights 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."
    • An article and video entitled "A Protocol for Computer-Based Protein Structure and Function Prediction" at the Journal of Visualized Experiments illustrates and dicusses the use of the I-TASSER server for protein structure and function prediction.
    • Feb. 2011 Biotechniques article about the P.I. behind this server, Yang Zhang.
  • Phyre server
  • Course on Homology Modeling
  • Class on Homology Modeling
  • Biskit that uses python for homology modeling
  • note on Pymol for homology modeling
  • For those without close homologs for homology modeling, I suggest I-Tasser or RaptorX for structure prediction.
  • Good summary of the best groups and servers from the CASP8 results
  • The HADDOCK web server is web server for data-driven biomolecular docking for modeling of biomolecular complexes.

• • EVfold at EVolutionary Couplings server. EVolutionary Couplings server provides functional and structural information about proteins derived from the evolutionary sequence record using methods from statistical physics.

• RNA modeling
  • Secondary Structure
    • The methods page for CompaRNA lists and provides links to several software and server-based programs for secondary structure prediction.
    • NASP is a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. See the companion article.
  • 3D Structure
    • ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. Related to this is ModeRNA, which is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence and allows for nucleotide modifications. See the companion article for the server.
    • 3dRNA also uses templates but you don't have control in specifying it. You upload a sequence and a secondary structure and if there is a reasonable template it will run and give you the resulting model.
• Nucleic Acid-protein modeling
  • The software page at the Bujnicki Laboratory website hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion article.
  • The HADDOCK web server is web server for data-driven biomolecular docking for modeling of biomolecular complexes.

• Quality Assessment
  • SMQQ , learn about it at SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

See 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.