Encontrados 15 documentos, a visualizar página 1 de 2
Predicting the secondary structure of proteins using Machine Learning algorithms
Rui Camacho; Rita Ferreira; Natacha Rosa; Vânia Guimarães; Nuno A. Fonseca; Vítor Santos Costa; Miguel de Sousa; Alexandre MagalhãesThe functions of proteins in living organisms are related to their 3-D structure, which is known to be ultimately determined by their linear sequence of amino acids that together form these macromolecules. It is, therefore, of great importance to be able to understand and predict how the protein 3Dstructure arises from a particular linear sequence of amino acids. In this paper we report the application of Machi...
Amino Acid Pair- and Triplet-wise Groupings in the Interior of Alpha-Helical Se...
Miguel M de Sousa; Cristian R Munteanu; Alejandro Pazos; Nuno A Fonseca; Rui Camacho; Alexandre MagalhãesA statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix ...
PopAffiliator: online calculator for individual affiliation to a major populati...
Luísa Pereira; Farida Alshamali; Rune Andreassen; Ruth Ballard; Wasun Chantratita; Nam Soo Cho; Clotilde Coudray; Jean-Michel Dugoujon; Marta EspinozaBecause of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, willnot allow to change this picture in the near future, notwithstanding the technologi...
Partitional Clustering of Protein Sequences - An Inductive Logic Programming Ap...
Nuno A. Fonseca; Vítor Santos Costa; Rui Camacho; Cristina Vieira; Jorge VieiraWe present a novel approach to cluster sets of protein sequences, based on Inductive Logic Programming (ILP). Preliminary results show that the method proposed produces understandable descriptions/ explanations of the clusters. Furthermore, it can be used as a knowledge elicitation tool to explain clusters proposed by other clustering approaches, such as standard phylogenetic programs.
Visually Guiding and Controlling the search while Mining Chemical Structures
Max Pereira; Vítor Santos Costa; Rui Camacho; Nuno A. FonsecaIn this paper we present the work in progress on LogCHEM, an ILP based tool for discriminative interactive mining of chemical frag- ments. In particular, we describe the integration with a molecule visual- isation software that allows the chemist to graphically control the search for interesting patterns in chemical fragments. Furthermore, we show how structured information, such as rings, functional groups lik...
Improving the Efficiency of ILP Systems
Nuno A. Fonseca; Vítor Santos Costa; Ricardo Rocha; Rui Camacho; Fernando SilvaInductive Logic Programming (ILP) is a sub-field of Machine Learning that provides an excellent framework for Multi-Relational Data Mining applications. The advantages of ILP have been successfully demonstrated in complex and relevant industrial and scientific problems. However, to produce valuable models, ILP systems often require long running times and large amounts of memory. In this article we address funda...
Parallel ILP for Distributed-Memory Architectures
Nuno A. Fonseca; Ashwin Srinivasan; Fernando Silva; Rui CamachoThe growth of machine-generated relational databases, both in thesciences and in industry, is rapidly outpacing our ability to extract useful information from them by manual means. This has brought into focus machine learning techniques like Inductive Logic Programming (ILP) that are able to extract humancomprehensible models for complex relational data. The price to pay is that ILP techniques are not ecient: t...
LogCHEM: Interactive Discriminative Mining of Chemical Structure
Vítor Santos Costa; Nuno A Fonseca; Rui CamachoOne of the most well known successes of Inductive Logic Programming (ILP) is on Structure-Activity Relationship (SAR) problems. In such problems, ILP has proved several times to be capable of constructing expert comprehensible models that help to explain the activity of chemical compounds based on their structure and properties. However, despite its successes on SAR problems, ILP has severe scalability problems...
K-RNN: k-Relational Neareast Neighbour Algorithm
Nuno A Fonseca; Vítor Santos Costa; Rui CamachoThe amount of data collected and stored in databases is growing considerably in almost all areas of human activity. In complex applications the data involves several relations and proposionalization is not a suitable approach. Multi- Relational Data Mining algorithms can analyze data from multiple relations, with no need to transform the data into a single table, but are computationally more expensive. In this ...
A study on amino acid pairing at the N- and C-termini of helical segments in pr...
Nuno A. Fonseca; Rui Camacho; Alexandre MagalhãesA systematic survey was carried out in an unbiased sample of 815 protein chains with a maximum of 20% homology selected from the Protein Data Bank, whose structures were solved at a resolution higher than 1.6 A ° and with a R-factor lower than 25%. A set of 5556 subsequences with a-helix or 310-helix motifs was extracted from the protein chains considered. Global and local propensities were then calculated for ...
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