Homology Modeling

Homology Modeling

Automated Servers

Program ICM
Program Modeller.

MODELLIST SELECTION OF THE BEST MODEL FROM MODELLER. This server sorts out the models produced by MODELLER acording with a calculation that considers the energies and the violations of each model. The lower the score the better the model. The program needs the 'log' file from MODELLER and it recognices versions 4 and 6.

EsyPred 3D Emphasis on alignments and then built by Modeller. enter sequence input
output

Swiss-model What-if. enter sequence input
output

SDSC1 enter sequence input
output

Predict Protein enter sequence input
output

3D-JIGSAW Comparative Modelling Server BioMolecular Modelling Group; Imperial Cancer Research Fund; London, UK. enter sequence input
output

CPHmodels Centre for Biological Sequence Analysis; The Technical University of Denmark; Denmark. enter sequence input
output

Consensus Boston University. enter sequence input
output

Unix based programs Scott Presnell. Hom. Mod. Using Midas.

JACKAL A package for protein structure modeling with BINGO as its graphic environment. Current version is 1.5 as of Oct, 20, 2002.

Wloop To predict protein loop backbone structures from their sequences and their flank backbone structures.

Bork group server Find structural homologs. enter sequence input
output

Homology Models Databases

ModBase

3D Crunch

DALi Find Structure Database.

Fold recognition

3D-PSSM

GenTHREADER Brunel University.

TOPITS PredictProtein server at EMBL.

UCLA-DOE

3D-PSSM

Structure Evaluation

EVA
EVA continously and automatically analyses protein structure prediction servers in 'real time' Columbia & Rockefeller Univ, New York.

Biotech Validation Suite for Protein Structures Runs Procheck, Prove and WhatIf; EBI & EMBL-Heidelberg.

WhatCheck/WhatIf Gert Vriend's protein structure analysis & verification tools Nijmegen, NL.

Primer Design

PCR PRIMER DESIGN AND REACTION OPTIMISATION

primer design criteria and software

Program ICM	Program Modeller.
MODELLIST	SELECTION OF THE BEST MODEL FROM MODELLER. This server sorts out the models produced by MODELLER acording with a calculation that considers the energies and the violations of each model. The lower the score the better the model. The program needs the 'log' file from MODELLER and it recognices versions 4 and 6.
EsyPred 3D	Emphasis on alignments and then built by Modeller.	enter sequence	input output
Swiss-model	What-if.	enter sequence	input output
SDSC1		enter sequence	input output
Predict Protein		enter sequence	input output
3D-JIGSAW Comparative Modelling Server	BioMolecular Modelling Group; Imperial Cancer Research Fund; London, UK.	enter sequence	input output
CPHmodels	Centre for Biological Sequence Analysis; The Technical University of Denmark; Denmark.	enter sequence	input output
Consensus	Boston University.	enter sequence	input output
Unix based programs	Scott Presnell. Hom. Mod. Using Midas.
JACKAL	A package for protein structure modeling with BINGO as its graphic environment. Current version is 1.5 as of Oct, 20, 2002.
Wloop	To predict protein loop backbone structures from their sequences and their flank backbone structures.
Bork group server	Find structural homologs.	enter sequence	input output

3D-PSSM
GenTHREADER	Brunel University.
TOPITS	PredictProtein server at EMBL.
UCLA-DOE
3D-PSSM

EVA	EVA continously and automatically analyses protein structure prediction servers in 'real time' Columbia & Rockefeller Univ, New York.
Biotech Validation Suite for Protein Structures	Runs Procheck, Prove and WhatIf; EBI & EMBL-Heidelberg.
WhatCheck/WhatIf	Gert Vriend's protein structure analysis & verification tools Nijmegen, NL.