The main task of this project was to study new approaches and strategies using pattern recognition techniques to improve aspects in the field of bioinformatics and computational biology.
Protein structure define its biological behavior. We worked to identify recurrent motifs, dealing with proteins as a cloud of segments, expecting big data. Our goal was to discover new motifs with an innovative geometrical method.
We applied segmentation algorithms to search areas of interest (active sites) in protein.



Extended Gaussian image: Histogram of the orientations of a surface represented on a unitary sphere and comparison Pocket - Ligand.



We aligned the models for the docking protein-ligand.

Using Hough Transform we developed the Cross Motif Search algorithm with MP and MPI for parallelism.



Motif Visualizer is an Open Source OpenGL GUI to improve usability, developed in collaboration and validation with biologists.

Related publications

• Marco Ferretti, Luigi Santangelo, Mirto Musci (2019). Optimized cloud based scheduling for protein secondary structure analysis, in The Journal of Supercomputing, v. 75, n. 7, pp. 3499-3520.
• Mirto Musci, Virginio Cantoni, Teo Argentieri (2017). MotifVisualizer: an interdisciplinary GUI for geometrical motif retrieval in proteins, in Proceedings - International Workshop on Database and Expert Systems Applications, DEXA-BIOKDD’16, pp. 64–68, DOI:10.1109/DEXA.2016.028
• Marco Ferretti, Mirto Musci, Luigi Santangelo (2015). Mpi-cms: a hybrid parallel approach togeometrical motif search in proteins, in Concurrency and Computation: Practiceand Experience, 27(18), pp. 5500–5516.
• Marco Ferretti, Mirto Musci (2015). Geometrical Motifs Search in Proteins: A Parallel Approach, in Parallel Computing, 42, pp. 60–74.
• Marco Ferretti, Mirto Musci, Luigi Santangelo (2014). A Hybrid Openmp and OpenmpiApproach to Geometrical Motif Search in Proteins, in Proceedings of theIEEE International Conference on Cluster Computing (IEEE Cluster 2014), IEEE Computer Society, pp. 298–304.
• Virginio Cantoni, Marco Ferretti, Nicola Pellicanó, Jennifer Vandoni, Mirto Musci, Nahumi Nugrahaningsih (2014). Protein Motif Retrieval by Secondary Structure Element Geometryand Biological Features Saliency, in 25^th International Workshop onDatabaseand Expert Systems Applications (DEXA), IEEE, 2014, pp. 23–27.
• Marco Ferretti, Mirto Musci (2013). Entire Motifs Search of Secondary Structures in Proteins: a Parallelization Study, in Proceedings of the 20^th European MPI Users’ Group Meeting, ACM Digital Library, pp. 199–204.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2013). 3D protein surface segmentation through mathematical morphology, Biomedical Engineering Systems and Technologies, Revised Selected Papers of 4^th International Joint Conference, BIOSTEC 2011, Rome, Italy, 26-29 January 2011, in Communications in Computer and Information Science, vol 273, pp. 97-109, ISBN:978-3-642-29751-9 (Print) 978-3-642-29752-6 (Online)
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak, Alfredo Petrosino (2013). Protein Motifs Retrieval By SS Terns Occurrences, in Pattern Recognition Letters, Elsevier, vol. 34, pp. 559-563, ISSN:0167-8655.
• Piercarlo Dondi, Luca Lombardi (2013). Essay: High performance computing for structural biology, Definitions: GPU, in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Luca Lombardi, Alessandro Gaggia (2013). Essay: Concavity tree for protein-protein interaction analysis, Definitions: Concavity Tree; in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Luca Lombardi, Riccardo Gatti (2013). Essay: Distance transform and travel depth, Definitions: Digital metrics; Distance Transform; in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Luca Lombardi, Alessandro Gaggia (2013). Essay: Extended Gaussian Image for pocket-ligand matching, Definitions: EGI; CEGI e ECEGI; in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Mattia E. (2013). Essay: Hough transform for structural motif retrieval, Definitions: Hough Transform; Range Tree; in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2013). Essay: Mathematical morphology for protein surface modeling, Definitions: Mathematical morphology; Basic Operators: Erosion, Dilation, Opening and Closing operators; in Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota Eds., Springer Science+Business Media LLC.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Protein structural blocks representation and search through unsupervised NN, 22^nd International Conference on Artificial Neural Networks - ICANN'12, 11-14 September 2012, Lausanne, SWITZERLAND, vol. 7553, p. 515-522, Springer, ISBN:9783642332661.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Structural Analysis of Protein Secondary Structure by GHT, 21^st International Conference on Pattern Recognition - ICPR'12, 11-15 Novembre 2012, Tsukuba, JAPAN, p. 1767-1770, IEEE Computer Society Press, ISBN:9784990644116.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Search of Protein Structural Blocks through Secondary Structure Triplets, 3^rd International Conference on Image Processing Theory, Tools and Applications - IPTA'12, 15-18 October 2012, Istanbul, Turkey, IEEE Press, pp. 222-226, ISBN:9781467325844.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Protein structural motifs search in Protein Data Base, International Conference on Computer Systems and Technologies - CompSysTech'12, 22-23 June 2012, Ruse, Bulgaria, Best Paper Award on session "Application Aspects", ACM Press, pp. 275-281, ISBN:9781450311939.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Motif Retrieval by Exhaustive Matching and Couple Co-occurrences, 9^th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics - CIBB'12, 12-14 July 2012, Texas, ISBN:9788890643712.
• Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Structural Biology and Pattern Recognition, Convegno GIRPR'12, May 21-23, Siena, n. 14, 9 pages.
• Virginio Cantoni, Alessio Ferone, Romina Oliva, Alfredo Petrosino (2012). Protein Gaussian Image (PGI): a protein structural representation based on the spatial attitude of secondary structure, in New Tools and Methods for Pattern Recognition in Complex Biological Systems, Nuovo Cimento C, Vol. 35, N. 5, Suppl. 1.
• Virginio Cantoni, Alessio Ferone, Alfredo Petrosino (2012). Protein motif retrieval through secondary structure spatial co-occurrences, in New Tools and Methods for Pattern Recognition in Complex Biological Systems, Nuovo Cimento C, Vol. 35, N. 5, Suppl. 1, 2012.
• Virginio Cantoni, Elio Mattia (2012). Protein structure analysis through Hough transform and range tree, in New Tools and Methods for Pattern Recognition in Complex Biological Systems, Nuovo Cimento C, Vol. 35, N. 5, Suppl. 1.
• Virginio Cantoni, Alessandro Gaggia, Luca Lombardi (2012). A data structure for protein-ligand morphological matching, in New Tools and Methods for Pattern Recognition in Complex Biological Systems, Nuovo Cimento C, Vol. 35, N. 5, Suppl. 1.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2012). Analysis of geometrical and topological aptitude for protein-protein interaction, in New Tools and Methods for Pattern Recognition in Complex Biological Systems, Nuovo Cimento C, Vol. 35, N. 5, Suppl. 1.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2011). Morphological analysis of 3D proteins structure, in Proceedings of Bioinformatics 2011, Part of BIOSTEC 2011, Roma (IT), 26-29 January 2011, pp. 15-21, ISBN:978-989-8425-36-2.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2010). Segmentation of SES for protein structure analysis, in Proceedings of Bioinformatics 2010, Part of BIOSTEC 2010, Valencia (ES), 20-23 January 2010, pp. 83-89, ISBN/ISSN:978-989-674-019-1.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2010). Proteins pockets analysis and description, in Proceedings of Bioinformatics 2010, Part of BIOSTEC 2010, Valencia (ES), 20-23 January 2010, pp. 211-216, ISBN/ISSN:978-989-674-019-1.
• Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2009). Towards Protein Interaction Analysis through Surface Labeling, in Proceedings of the 15^th International Conference of Image Analysis and Processing - ICIAP 2009, Vietri sul Mare (IT), Sep 8-11, 2009, pp. 604-612, ISBN/ISSN:978-3-642-04145-7.