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CombFunc: predicting protein function using heterogeneous data sources

Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web ...

PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

Motivation: Analysis of protein–protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction. Method and ...

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity ...

3DLigandSite: predicting ligand-binding sites using similar structures

Mark N. Wass 0 Lawrence A. Kelley 0 Michael J. E. Sternberg 0 0 Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London , London , SW7 2AZ, UK 3DLigandSite is a web

3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Victor I. Lesk 0 Michael J. E. Sternberg 0 Associate Editor: Burkhard Rost 0 Division of Molecular Biosciences, Imperial College London , South Kensington, London SW72AZ, UK Motivation: Reliable

ConFunc—functional annotation in the twilight zone

Mark N. Wass 0 Michael J. E. Sternberg 0 Associate Editor: Dmitrij Frishman 0 Structural Bioinformatics Group , Biochemistry Building , Division of Molecular Biosciences, Imperial College London

Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

Motivation: Databases of sequenced genomes are widely used to characterize the structure, function and evolutionary relationships of proteins. The ability to discern such relationships is widely expected to grow as sequencing projects provide novel information, bridging gaps in our map of the protein universe. Results: We have plotted our progress in protein sequencing over the ...

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Z. N. Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J. E. Sternberg Mark N. Wass Rachael P. Huntley Maria J. Martin Claire O'Donovan Peter N

Prediction of viable circular permutants using a graph theoretic approach

Motivation: In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting ...

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Genome3D, available at, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural ...

Capturing expert knowledge with argumentation: a case study in bioinformatics

Motivation: The output of a bioinformatic tool such as BLAST must usually be interpreted by an expert before reliable conclusions can be drawn. This may be based upon the expert’s experience, additional data and statistical analysis. Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where ...

3D‐GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes

The 3D‐GENOMICS database ( provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence ...

SAWTED: Structure Assignment With Text Description—Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons

Robert M. MacCallum 0 Lawrence A. Kelley 0 Michael J. E. Sternberg 0 0 Biomolecular Modelling Laboratory, Imperial Cancer Research Fund , 44 Lincoln's Inn Fields, London WC2A 3PX, UK Motivation

ArchDB: automated protein loop classification as a tool for structural genomics

The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super‐secondary structural motifs, consisting of a few secondary ...

Isolation of a small molecule inhibitor of DNA base excision repair

The base excision repair (BER) pathway is essential for the removal of DNA bases damaged by alkylation or oxidation. A key step in BER is the processing of an apurinic/apyrimidinic (AP) site intermediate by an AP endonuclease. The major AP endonuclease in human cells (APE1, also termed HAP1 and Ref-1) accounts for >95% of the total AP endonuclease activity, and is essential for the ...