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The function of a protein is closely correlated with its subcellular location. With the rapid increase in new protein sequences entering into data banks, we are confronted with a challenge: is it possible to utilize a bioinformatic approach to help expedite the determination of protein subcellular locations? To explore this problem, proteins were(More)
Given a nascent protein sequence, how can one predict its signal peptide or "Zipcode" sequence? This is a first important problem for scientists to use signal peptides as a vehicle to find new drugs or to reprogram cells for gene therapy. Based on a model that takes into account the coupling effect among some key subsites, the so-called [-3, -1, +1](More)
All existing algorithms for predicting the content of protein secondary structure elements have been based on the conventional amino-acid-composition, where no sequence coupling effects are taken into account. In this article, an algorithm was developed for predicting the content of protein secondary structure elements that was based on a new(More)
Cells use a ZIP code system to sort newly synthesized proteins and deliver them wherever they are needed: into different internal compartments called organelles or even out of the cell altogether. One of the most essential features of the ZIP code system is the signal sequence or "address tag," which is originally present in the N-terminal part of the(More)
The structural class of a protein domain can be approximately predicted according to its amino acid composition. However, can the prediction quality be improved by taking into account the coupling effect among different amino acid components? This question has evoked much controversy because completely different conclusions have been obtained by different(More)
Support Vector Machines (SVMs) which is one kind of learning machines, was applied to predict the specificity of GalNAc-transferase. The examination for the self-consistency and the jackknife test of the SVMs method were tested for the training dataset (305 oligopeptides), the correct rate of self-consistency and jackknife test reaches 100% and 84.9%,(More)
The discriminant function algorithm was introduced to predict the subcellular location of proteins in prokaryotic organisms from their amino-acid composition. The rate of correct prediction for the three possible subcellular locations of prokaryotic proteins studied by Reinhardt and Hubbard (Nucleic Acid Research, 1998, 26:2230-2236) was 90% by the(More)
Tight turns play an important role in globular proteins from both the structural and functional points of view. Of tight turns, beta-turns and gamma-turns have been extensively studied, but alpha-turns were little investigated. Recently, a systematic search for alpha-turns was conducted by V. Pavone et al. [(1996) Biopolymers, Vol. 38, pp. 705-721] from 190(More)
Can the coupling effect among different amino acid components be used to improve the prediction of protein structural classes? The answer is yes according to the study by Chou and Zhang (Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995), but a completely opposite conclusion was drawn by Eisenhaber et al. when using a different dataset constructed by(More)