Proteomics and Bioinformatics

Description. The main task of this project is to study new approaches, strategies and capabilities of pattern recognition techniques for improving some aspects in the field of bioinformatics and computational biology. In particular modeling and comparison of proteins 3D structures will be considered. Considering the state of the art, it is scheduled to investigate three particular approaches that are not yet being followed (or just partially). 1) Usage of the generalized 3D Hough transform for protein comparison. The main scope of this topic is to search proteins structural similarities in database (PDB). This could be applied to different levels of protein representation (atomic, secondary structure or geometric 3D surfaces). Let's consider, for example, the secondary representation of a protein (made of Helix and Strand). Every detected "evidence" (say Helix or Strand) votes (with a weighted contribution) for a set of "edition" of the model each one corresponding to a given Helix or Strand of the searched protein. By collecting all the contribution, the edition of the model that gathers sufficient votes, determinates the similarity. Notice that G-Hough transform is a parallel algorithm (elements can vote in parallel, proteins can be compared in parallel ...). This could provide good performances on parallel architectures (like CELL BE processor). 2) Usage of the EGI (Extended Gaussian Images) or CEGI (Complex EGI) for solving proteins surface docking (protein-protein or protein-ligand). The objective here is to find complementary regions. EGI is the histogram of surface orientation represented on the unitary sphere. EGI are computationally simple to evaluate and therefore it is worth verifying if necessary condition for docking applied to EGI are enough selective. The Complex EGI is an enriched version in which the orientation is combined with the distance. The advantages/disadvantages of this different approach will be investigated. 3) Applying mathematical morphology (by Serra-Motheron - also known as "image algebra" for others) for surface modeling. The objective is to develop new computational methods that can be applied also to prediction and validation of protein-protein interactions. Simple operands like dilation or erosion can be applied to protein molecular surface modeling. An application can be a comparative analysis finalized to the individuation of topological regions preserved in different species.

Software.

"Protein Segmentation and Surface Analyzer"

"E.G.I. Protein Visualizer"

Publications.

Ferretti Marco, Santangelo Luigi, Musci Mirto (2019). Optimized cloud based scheduling for protein secondary structure analysis. In The Journal of Supercomputing, v. 75, n. 7, pp. 3499-3520.

Musci Mirto, Maruccia Gioele, Ferretti Marco (2019). A Review of Quasi perfect Secondary Structure Prediction Servers. In International Conference on Database and Expert Systems Applications, pp. 21-26.

Musci Mirto, Ferretti Marco (2018). Mining geometrical motifs co-occurences in the CMS dataset. In International Conference on Database and Expert Systems Applications, pp. 179-190.

Musci Mirto, Ferretti Marco (2018). Mining Geometrical Motifs Co-occurrences in the CMS Dataset, DEXA 2018 International Workshops, BDMICS, BIOKDD, and TIR, Regensburg, Germany, 3–6 September 2018, in Database and Expert Systems Applications, pp.179-190, DOI:10.1007/978-3-319-99133-7_15

Argentieri Teo, Cantoni Virginio, Musci Mirto (2017). Extending Cross Motif Search with heuristic data mining. In Proceedings of 28th International Workshop on Database and Expert Systems Applications, IEEE Computer Society, Washington (USA).

Musci Mirto, Cantoni Virginio, Argentieri Teo (2016). MotifVisualizer: an interdisciplinary GUI for geometrical motif retrieval in proteins. In Proceedings of 27th International Workshop on Database and Expert Systems Applications, IEEE Computer Society, Washington (USA), DEXA-BIOKDD’16, DOI:10.1109/DEXA.2016.028

Cantoni Virginio, Ferretti Marco, Musci Mirto, Nugrahaningsih Nahumi (2015). Structural Motifs Identification and Retrieval: A Geometrical Approach. In M. Elloumi, C. S. Iliopoulos, J. T. L. Wang, A. Y. Zomaya (Eds.), Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, 1st edition, John Wiley and Co., New York, USA.

Ferretti Marco, Musci Mirto, Santangelo Luigi (2015). Mpi-cms: a hybrid parallel approach togeometrical motif search in proteins. In Concurrency and Computation: Practiceand Experience, 27 (18), pp. 5500–5516.

Ferretti Marco, Musci Mirto (2015). Geometrical Motifs Search in Proteins: A Parallel Approach. In Parallel Computing, 42, pp. 60–74.

Virginio Cantoni (2014). Pattern Recognition Tools for Proteomics. The European Physical Journal Plus, Vol. 129, N. 130, pp. 1-2, ISSN 2190-5444, DOI:10.1140/epjp/i2014-14130-3.

Ferretti Marco, Musci Mirto, Santangelo Luigi (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.

Cantoni V., Ferretti M., Pellicanó N., Vandoni J., Musci M., Nugrahaningsih N. (2014). Protein Motif Retrieval by Secondary Structure Element Geometryand Biological Features Saliency. In 25th International Workshop onDatabaseand Expert Systems Applications (DEXA), IEEE, 2014, pp. 23–27.

Ferretti Marco, Musci Mirto (2013). Entire Motifs Search of Secondary Structures in Proteins: a Parallelization Study. In Proceedings of the 20th European MPI Users’ Group Meeting, ACM Digital Library, pp. 199–204.

Drago G., Ferretti M., Musci M. (2013). CCMS: A Greedy Approach to MotifExtraction. In New Trends in Image Analysis and Processing — ICIAP 2013, Vol. 8158 of Lecture Notes in Computer Science, Springer, Heidelberg, pp. 363–371.

Virginio Cantoni, Riccardo Gatti, Luca Lombardi (2013). 3D protein surface segmentation through mathematical morphology. In Biomedical Engineering Systems and Technologies. Revised Selected Papers of 4th International Joint Conference, BIOSTEC 2011, Rome, Italy, January 26-29, 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). Searching Structural Blocks by SS Exhaustive Matching. Lecture Notes in Bionformatics 5381, Leif Peterson, Giuseppe Russo, Francesco Masulli Eds., CIBB 2012, LNBI 7845, Springer-Verlag, pp. 57-69.

Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak, Alfredo Petrosino (2013). Protein Motifs Retrieval By SS Terns Occurrences. Pattern Recognition Letters, Elsevier, vol. 34, pp. 559-563, ISSN: 0167-8655.

Cantoni V., Lombardi L., Gaggia A. (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.

Cantoni V., Gatti R., Lombardi L. (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. In 22nd International Conference on Artificial Neural Networks, ICANN'12, September 11-14, 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. In 21st International Conference on Pattern Recognition, ICPR'12, November 11-15, 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. In 3rd International Conference on Image Processing Theory, Tools and Applications, IPTA'12, October 15-18, 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. In International Conference on Computer Systems and Technologies, CompSysTech'12, June 22-23, 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. In 9th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB'12, July 12-14, Texas, ISBN: 9788890643712.

Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak and Alfredo Petrosino (2012). Structural Biology and Pattern Recognition. In Convegno GIRPR'12, May 21-23, Siena, n. 14, 9 pages.

V. Cantoni, A. Ferone, R. Oliva, A. 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.

V. Cantoni, A. Ferone, A. 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.

V. Cantoni, E. 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.

V. Cantoni, A. Gaggia, L. 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.

V. Cantoni, R. Gatti, L. 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). Jan 26-29, 2011. (pp. 15-21). ISBN: 978-989-8425-36-2.

Virginio Cantoni, Alessandro Gaggia, Riccardo Gatti, Luca Lombardi. (2011). Geometrical constraints for ligand positioning. In Proceedings of Bioinformatics 2011, Part of BIOSTEC 2011, Roma (IT), Jan 26-29, 2011 (pp. 204-209), ISBN: 978-989-8425-36-2

Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2010). Segmentation of SES for protein structure analysis. In Proceedings of the 1st International Conference on Bioinformatics. BIOSTEC 2010. Valencia (ES), Jan 20-23, 2009 (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 the 1st International Conference on Bioinformatics. BIOSTEC 2010. Valencia (ES), Jan 20-23, 2009 (pp. 211-216), ISBN/ISSN 978-989-674-019-1

Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2010). Approaches for Protein Surface Curvature Analysis. Submitted to Pattern Analysis and Applications Journal

Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2009). Towards Protein Interaction Analysis through Surface Labeling. In Proceedings of the 15th 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