Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network.

Tópicos

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Resumo

The PDZ domain of proteins mediates a protein-protein interaction by recognizing the hydrophobic C-terminal tail of the target protein. One of the challenges put forth by the DREAM (Discussions on Reverse Engineering Assessment and Methods) 2009 Challenge consists of predicting a position weight matrix (PWM) that describes the specificity profile of five PDZ domains to their target peptides. We consider the primary structures of each of the five PDZ domains as a numerical sequence derived from graph-theoretic models of each of the individual amino acids in the protein sequence. Using available PDZ domain databases to obtain known targets, the graph-theoretic based numerical sequences are then used to train a neural network to recognize their targets. Given the challenge sequences, the target probabilities are computed and a corresponding position weight matrix is derived. In this work we present our method. The results of our method placed second in the DREAM 2009 challenge.

Resumo Limpo

pdz domain protein mediat proteinprotein interact recogn hydrophob ctermin tail target protein one challeng put forth dream discuss revers engin assess method challeng consist predict posit weight matrix pwm describ specif profil five pdz domain target peptid consid primari structur five pdz domain numer sequenc deriv graphtheoret model individu amino acid protein sequenc use avail pdz domain databas obtain known target graphtheoret base numer sequenc use train neural network recogn target given challeng sequenc target probabl comput correspond posit weight matrix deriv work present method result method place second dream challeng

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