Research Topics
| D W RitchieSummaryAffiliation: University of Aberdeen Country: UK Publications
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Detail Information
Publications
Modelling antibody side chain conformations using heuristic database searchD W Ritchie
Department of Computing Science, King s College, University of Aberdeen, UK
Proc Int Conf Intell Syst Mol Biol 5:237-40. 1997..We expect our approach could be used with other homologous protein families, in addition to antibodies, both to improve the quality of model structures and to give a "smart start" to the side chain placement problem...- Protein docking using spherical polar Fourier correlationsD W Ritchie
Department of Computing Science, King s College, University of Aberdeen, Aberdeen, United Kingdom
Proteins 39:178-94. 2000..The correct conformation of the complex is frequently identified when docking bound subunits, and a good docking orientation is ranked within the top 20 in 11 out of 18 cases when starting from unbound subunits. Proteins 2000;39:178-194... - Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2David W Ritchie
Department of Computing Science, King s College, University of Aberdeen, Aberdeen, United Kingdom
Proteins 52:98-106. 2003..This finding shows that useful in silico protein-protein docking predictions can now be made with increasing confidence, even for very large macromolecular complexes... - Recent progress and future directions in protein-protein dockingDavid W Ritchie
Department of Computing Science, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK
Curr Protein Pept Sci 9:1-15. 2008.... - Docking essential dynamics eigenstructuresDiana Mustard
Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK
Proteins 60:269-74. 2005..Some suggestions to improve this promising new approach are presented... - Analysis of fish IL-1beta and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: implications for pharmacological designAntonis I Koussounadis
Department of Computing Science, King s College, University of Aberdeen, Aberdeen AB24 3UE, UK
Curr Pharm Des 10:3857-71. 2004..Further analysis of the IL-1 system may prove useful in engineering IL-1 with improved features and in suggesting new avenues for therapeutic intervention... 
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functionsDavid W Ritchie
Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK
Bioinformatics 24:1865-73. 2008..Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available...- Toward high throughput 3D virtual screening using spherical harmonic surface representationsLazaros Mavridis
Department of Computing Science, King s College, University of Aberdeen, Aberdeen AB24 3UE, UK
J Chem Inf Model 47:1787-96. 2007..The approach described is currently being extended to allow the rapid search and comparison of arbitrary combinations of molecular surface properties... - HexServer: an FFT-based protein docking server powered by graphics processorsGary Macindoe
Department of Computing Science, Lillybank Gardens, University of Glasgow, G12 8QQ Scotland, UK
Nucleic Acids Res 38:W445-9. 2010..The server is publicly available and does not require any registration or identification by the user... 
Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor dockingVioleta I Pérez-Nueno
Grup d Enginyeria Molecular, Institut Quimic de Sarria IQS, Universitat Ramon Llull, Barcelona, Spain
J Chem Inf Model 48:509-33. 2008..The results obtained for CCR5 suggest the possibility that different active scaffolds bind in different ways within the CCR5 pocket...