There are various fold recognition and homology modelling algorithms available as web servers. Make use of the links (and any other servers you find useful) to deduce as much as you can about the following sequences. Dont forget to make use of sequence search methods and secondary structure predictions to reach your decision.

Fold Recognition and Homology Modelling Targets

So start here ... NCBI Blast

Useful Links

Fold Recognition Servers

3DPSSM
Based on sequence profiles, solvatation potentials and secondary structure.

SAMT02
The query is checked against a library of hidden Markov models. This is NOT a threading technique, it is sequence based.

GenTHREADER
Combines profiles and sequence-structure alignments. A neural network-based jury system calculates the final score based on solvation and pair potentials.

FUGUE
FUGUE uses environment-based fold profiles that are created from structural alignments. Gap penalties are environment dependent.

FFAS03
This is a variant of FFAS, which aligns profile to profile. Profiles are generated differently from PSI-BLAST. You need to register to use it.

More Fold Recognition Servers Here

Metaservers

These are servers that make their predictions based on the results of two or more different methods. Some simply look for the consensus prediction between several methods while others calculate their own scores based on the results that they get back from the servers.

3D Jury
Uses the results of a huge range of fold recognition servers to make its predictions. Large choice on the web page ... ! FFAS, 3DPSSM, Pcons (a metaserver itself!), GenTHREADER, INBGU, SAMT99, FUGUE y ORFeus.

LIBELLULA
This is our own metaserver. Currently makes a selection between the results from just the 3DPSSM and SAM T02 servers. Uses its own neural network to rate the predictions.



Homology Modelling Servers

SWISS-MODEL
SWISS-MODEL is an automated comparative modelling server (ExPASy, CH)

SDSC1
Protein structure homology modelling server (San Diego, USA)

3D-JIGSAW
Automated system for 3D models for proteins (Cancer Research UK)

WHATIF
WHAT IF Web interface: homology modelling, drug docking, electrostatics calculations, structure validation and visualisation. You have to provide your own alignments to build models.

ROBETTA
Robetta is a full-chain protein structure prediction server. It divides protein chains into domains, and models them by either homology modelling or ab initio modelling.




Other Useful Servers

CA-GEN
A server that can generate CA trace for models from any fold recognition (or other) alignment. Combine the output with MaxSprout to generate all atom models.

Fold to 3D Model Converter
A server that will convert alignment style models to actual PDB type 3D models

MaxSprout
A server that will add side chains to CA traces

SQUARE
A server that will check how good your homology modelling or fold recogniton alignment is (CNB, Madrid).

Loops Database
A table of five protein loop classes. (Cancer Research UK)

BIOTECH Validation Suite
An evaluation suite that uses three widely available validation programs (PROCHECK, PROVE and WHAT IF)

Verify3D
A tool designed to help in the refinement of crystallographic structures. It also provides a visual analysis of model quality.

PDG-MAMMOTH
A local method for evaluating RMSD between model and the actual target protein

CAFASP Server Comparison
Compare Your Predictions Here!!