HOMOLOGY MODELLING

Michael Tress
Protein Design Group.
Centro Nacional de Biotecnologia (C.N.B.- C.S.I.C.)
Campus Universidad Autonoma.Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854570. Fax: +34-91-5854506.
Madrid-May-05

EXAMPLES

For those who would like a review of comparative modelling, there is a walk through example of SWISS MODEL in action and some exercises here.

SERVERS

Send your sequences to some of these servers. Note - you may only be able to model structures for certain domains.

  1. SWISS-MODEL SWISS-MODEL is an automated comparative modelling server (ExPASy, CH)
  2. CPHmodels Server using homology modelling (BioCentrum, Denmark)
  3. SDSC1 Protein structure homology modelling server (San Diego, USA)
  4. 3D-JIGSAW Automated system for 3D models for proteins (Cancer Research UK)
  5. WHATIF WHAT IF Web interface. You have to provide your own alignments to build models. Does homology modelling and structure validation.
  6. ROBETTA Not strictly a comparative modelling server. Robetta is a full-chain protein structure prediction server. It divides chains into domains, and models them by either homology modelling or ab initio modelling.

MODEL EVALUATION SERVERS

Check the quality of the model you receive back with these model evaluation servers.

  1. SIFT Protein Model Evaluation Server
  2. ProQ Protein Model Evaluation Server
  3. Verify 3D Protein Model Evaluation Server
  4. Procheck Protein Model Evaluation Server
  5. Rampage Analyses Ramachandran Plots

QUICK GUIDES