:: DESCRIPTION
MEPSA is a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MEPSA: minimum energy pathway analysis for energy landscapes.
Marcos-Alcalde I, Setoain J, Mendieta-Moreno JI, Mendieta J, Gómez-Puertas P.
Bioinformatics. 2015 Jul 31. pii: btv453.
:: DESCRIPTION
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).
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
:: DESCRIPTION
RNAenn computes the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.
Dotu I, Mechery V, Clote P.
PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412.
:: DESCRIPTION
The BEESEM program is designed for transcription factor binding motif discovery using HT-SELEX data.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2017 Aug 1;33(15):2288-2295. doi: 10.1093/bioinformatics/btx191.
BEESEM: estimation of binding energy models using HT-SELEX data.
Ruan S, Swamidass SJ, Stormo GD
:: DESCRIPTION
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
::DEVELOPER
Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh and Shashank Shekhar,
“Bhageerath-H: A homology ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins“,
BMC Bioinformatics, 2014, 15(Suppl 16):S7
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
Jayaram B, Bhushan K, Shenoy SR, Narang P, Bose S, Agrawal P, Sahu D, Pandey V.
Nucleic Acids Res. 2006;34(21):6195-204
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition.
Ahmad S, Kono H, Araúzo-Bravo MJ, Sarai A.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W124-7.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Camacho CJ and Zhang C (2005).
FastContact: rapid estimate of contact and binding free energies.
Bioinformatics, 21(10):2534-6.