NOTE: All the software available here comes unsupported and with no warranties.


A program to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput.

Details: ReadMe (http://protein NULL.puc NULL.html)
Download binary: Linux 2.4.2-2 (http://protein NULL.puc NULL.tar NULL.gz)
Authors: Melo, F., Feytmans, E.


STOVCA (STructural OVerlap CAlculator) is a software that takes as input a pairwise structure superposition of proteins, DNA or RNA in PDB format generated by any software and produces a standardized structural alignment and its corresponding similarity measures, according to the parameters provided by the user. Therefore, STOVCA allows the direct comparison and ranking of structural superpositions generated by any structure superposition software

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Authors: Slater, A.W., Castellanos, J., Sippl, M.J. and Melo, F.

PDIviz is a plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL. The plugin provides a total of nine distinct 3D visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type.

Web site: (http://melolab
Authors: Judemir Ribeiro, Francisco Melo and Andreas Schüller


This software calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) using a merged method that is based on three different thermodynamic tables.

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Authors: Panjkovich, A., Norambuena, T. and Melo, F.


MOMA (from MOrphing & MAtching) is a program that calculates fast and flexible comparison of protein structure chains. This method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm.

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Authors: Gutiérrez, F. I., Rodriguez-Valenzuela, F., Ibarra, I. L., Devos, D. P., & Melo, F.


StAR is a software that computes ROC curves and several related statistics to assess the significance of their differences in performance.

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Authors: Vergara, I.A., Norambuena, T., Ferrada, E., Slater, A.W. and Melo, F.


SAT (Sequence Alignment Teacher) is a software to teach about sequence alignment methods based on dynamic programming such as Smith – Waterman (Local) and Needleman – Wunsch (Global).

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Authors: Ibarra, I and Melo, F.