Program enoLOGOS generates LOGOs of transcription factor DNA binding sites from various types of input matrices. It can utilize standard count matrices, probability matrices or matrices of “energy” values (i.e., log-frequencies).
Bhageerath is an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2-3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3-6 A RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures.
BHAGEERATH-H is a homology ab-intio hybrid eeb server for protein tertiary structure prediction
ReadOut is a server calculates:
(1) The DNA conformational energy and Z-score, and
(2) The direct readout or base-amino acid interaction energy and Z-score for protein-DNA complex structures.
FastContact provides a fast estimate of the interaction free energy between two proteins. Because it is based on folding data, the estimate is robust and does not require to be re-parameterized as more complex structures become available.