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During the course of TREC{1 the low-level search functions were split o into a separate Basic Search System (BSS) [2], but retrieval and ranking of documents was still done using the \classical" probabilistic model of Robertson and Sparck Jones[7] with no account taken of document length or term frequency within document or query. Four runs were submitted(More)
SUMMARY The PROTORP server analyses protein-protein associations in 3D structures. The server calculates a series of physical and chemical parameters of the protein interaction sites that contribute to the binding energy of the association. These parameters include, size and shape, intermolecular bonding, residue and atom composition and secondary structure(More)
A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding(More)
MOTIVATION All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein(More)
Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three(More)
The PiRaNhA web server is a publicly available online resource that automatically predicts the location of RNA-binding residues (RBRs) in protein sequences. The goal of functional annotation of sequences in the field of RNA binding is to provide predictions of high accuracy that require only small numbers of targeted mutations for verification. The PiRaNhA(More)
This paper reports on City University's work on the TREC{2 project from its commencement up to November 1993. It includes many results which were obtained after the August 1993 deadline for submission of o cial results. For TREC{2, as for TREC{1, City University used versions of the Okapi text retrieval system much as described in [2] (see also [3, 4]).(More)