Our Programs

TF2DNA

Structure-based determination of transcription factor binding sites TF2DNA installation program

RF_HA_SRS RF_CB_SRS_OD

Statistical pair potentials

SmotifCOMP program

SmotifCOMP program (293M)

Smotif database

Smotif Database (MySQL, compressed, 428Mb!)

SmotifCOMPSuperfamilyNetwork

SmotifCOMP-based SCOP Superfamily network

SmotifCS

SMOTIFCS implement a hybrid protein modeling algorithms that relies on a library of protein super-secondary structure motifs (Smotifs) and easily obtainable NMR experimental data.

remodel_pdb

Software for remodeling the missing residues in the entire PDB, these remodeled structures can be used in the SmotifTF package.

SAMMI

MI-score calculates the average mutual information score for a given multipe sequence alignment.

Our Servers

BlastProfiler

Sequence alignment profile generator.

ModLoop

Modeling loops in protein structures.

Loop decoy sets

500-500 8 and 12 residue long, optimized loops for 40 proteins.

MMM server

Multiple Mapping Method: a sequence-to-structure alignment tool.

M4T server

Comparative Modelling using a combination of multiple templates and interative optimization of alternative alignments.

MMMTree server

Comparative Modelling using an iterative sequence to structure alignmnet approach.

ArchPred server

A template based loop structure prediction server.

Cysredox

Predicting oxidation states of Cys residues from sequences of proteins.

Autopublish

Web Tool to speed up protein structure publications and annotation.

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Fiser Lab