There are various fold recognition, hybrid sequence methods 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.
Try to predict structures for these sequences using the servers below: Target Sequences
So start here ... NCBI Blast
Useful Links if There is No Template with BLAST
1D Feature Prediction (inc. Secondary Structure)Fold Recognition and Hybrid Servers
3DPSSM
Based on sequence profiles, solvatation potentials and secondary structure.
PHYRE
The successor to 3DPSSM, a fragment-based assembler.
Dr. FRankensteins Toolbox
Another new server, tested in CASP, that did very well in the FR and CM categories, though it
still wasnt working last week.
SAMT02
The query is checked against a library of hidden Markov models.
This is a hybrid sequence technique, it is sequence based.
GenTHREADER/mGenTHREADER
Combines profiles and sequence-structure alignments. A neural network-based
jury system calculates the final score based on solvation and pair potentials.
SPARKS2
Top server in CM predictions in CASP 6. Sequence, secondary structure Profiles And Residue-level Knowledge-based Score for fold recognition.
SPARKS3
Sequence, secondary structure Profiles And Residue-level Knowledge-based Score for fold recognition. Better for harder targets.
ROBETTA
ROBETTA detects fragments with BLAST, FFAS03, or 3DJury, and generates alignments with K*SYNC. Loop regions are assembled from fragments and side chains using a replace and score method.
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.
Meta-Basic
Hybrid metaserver that uses a range of PSIBLAST profiles and secondary structure to make predictions
UCLA-DOE Structure
Prediction Server
Executes various fold recognition programs
and reports a consensus.
Raptor
Best in CAFASP 3 - you have to send an email to warn them first.
123D+
Combines
substitution matrix, secondary structure prediction, and contact capacity potentials.
Meta-servers
These are servers that make their predictions based on the results of two or more different methodss.
Some simply look for the consensus prediction between several methods while oters 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 secondary structure servers, fold recognition servers, hybrid servers and meta-servers to make its predictions. Predictions are scored by its own Jury system.
Servers used include PSIPRED, ProfSec, FFAS, 3DPSSM, GenTHREADER, INUB, SAMT02, FUGUE and META-BASIC
GeneSilico
Another metaserver that includes a range of secondary structure servers, fold recognition servers, hybrid servers and meta-servers to make its predictions. All you need is here ...
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.
INUB
The metaserver from the Fischer lab in Buffalo.
PCONS
The original metaserver that as well as a prediction can return a whole model based on PMOD.
SWISS-MODEL
SWISS-MODEL is an automated comparative modelling server (ExPASy, CH)
SDSC1
Protein structure homology modeling 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.
WHATIF
WHAT IF also can evaluate models and is probably the best of the servers for this.
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.
SIFT Protein Model Evaluation Server
ProQ Protein Model Evaluation Server
SQUARE
A server that will check how good your homology modelling or
fold recogniton alignment is (CNB, Madrid).
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.
MaxSprout
A server that will add side chains to CA traces
PDG-MAMMOTH
A local method for evaluating RMSD between model and the actual target protein