Contact Details
Senior Lecturer
Room 3B6 JMS Building
Department of Chemistry & Biochemistry
University of Sussex
Falmer, BN1 9QG
s.jones"at"sussex.ac.uk
Grants
- Medical Research Council: 2005-2008 (200K GBP) Functional Genomics: computational prediction of RNA-binding function from sequence.
- Royal Society: 2003-2004 (15K GBP)
Computational prediction of RNA-binding function from protein structure.
Publications
RNA-binding residues in sequence space: conservation and interaction patterns.
Spriggs RV & Jones S. (2009)
Computational Biology and Chemistry. In press.
Protein function annotation from sequence: prediction of residues interacting with RNA.
Spriggs RV, Murakami Y, Nakamura H & Jones S. (2009)
Bioinformatics 25 p25 p1492-1497.
ProtorP: A protein-protein interaction analysis server.
Reynolds C, Damerell D & Jones S. (2009)
Bioinformatics. 25 p413-414.
Evaluating conformational changes in protein structures binding RNA
Ellis J.J & Jones S. (2008)
Proteins: Structure, Function and Bioinformatics 70 p1518-26.
Computational and Structural Characterisation of Protein Associations
Jones S. (2008)
in Protein Dimerization (and oligomerization) in Biology. Editor J. Matthews. Landes BioScience
Protein-RNA Interactions: structural analysis and functional classes
Ellis J.J, Broom M. & Jones S. (2007)
Proteins: Structure, Function and Bioinformatics 66 p903-911.
PDF
Patch prediction of protein interaction sites: validation of a scoring function for an online server
Jones S & Murakami Y. (2007)
Lecture Notes in Bioinformatics LNBI 4414 p303-113
PDF
SHARP2: protein-protein interaction predictions using patch analysis
Murakami Y & Jones S. (2006)
Bioinformatics 22 p1794-1795
PDF
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Ferrer-Costa C, Shanahan, HP, Jones S & Thornton JM. (2005)
Bioinformatics 21 p3679-3680.
Identifying DNA binding proteins using structural motifs and the electrostatic potential
Shanahan HP. Garcia MA, Jones S & Thornton JM (2004)
Nucleic Acids Research 32 p4732-4741
An overview of basic helix-loop-helix proteins
Jones S (2004)
Genome Biology 5:226
Determination of protein charge by capillary zone electrophoresis
Winzor DJ, Jones S & Harding SE (2004)
Analytical Biochemistry 333 p225-229
Searching for functional sites in protein structures
Jones S & Thornton JM (2004)
Current Opinion in Chemical Biology 8 p3-7
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
Jones S, Shanahan H, Berman HM & Thornton JM (2003)
Nucleic Acids Research 31 p7189-7198
Using structural motifs to identify proteins with DNA binding function.
Jones S, Barker J, Nobeli I & Thornton JM (2003)
Nucleic Acids Research 31 p2811-2823
Protein-DNA interactions: the story so far and a new method for prediction
Jones S & Thornton JM (2003)
Comparative and Functional Genomics 4 p428-431
The cohesin complex: sequence homologies, interaction networks
and shared motifs
Jones S & Sgouros J. (2001)
Genome Biology 2 (3) 0009
Protein-RNA interactions: a structural analysis
Jones S, Daley DTA, Luscombe NM, Berman HM & Thornton JM. (2001)
Nucleic Acids Research 29 p943-954
Protein Domain Interfaces: characterisation and comparison
with oligomeric protein interfaces
Jones S, Marin A, & Thornton JM. (2000)
Protein Engineering 13 p77-82
Analysis and prediction of carbohydrate binding sites
Taroni C, Jones S, & Thornton JM. (2000)
Protein Engineering 13 p89-98
Novel Size-Independent Modeling of the Dilute Solution Conformation of the
Immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS
Carrasco B, Garcia de la Torre J, Byron O, King D, Walters C, Jones S & Harding SE. (1999)
Biophysical Journal 77 p2902-2910
COVOL: An interactive program for evaluating second virial
coefficients from the triaxial shape or dimensions of rigid macromolecules.
Harding SE, Horton JC, Jones S, Thornton JM & Winzor DJ. (1999)
Biophysical Journal 76 p2432-2438.
Protein-DNA Interactions: A Structural Analysis
Jones, S, van Heyningen P, Berman HM, Thornton, JM. (1999)
Journal of Molecular Biology 287 p877-896
Protein domains, folds and functions.
Jones S, Martin ACR, Karmirantzou M, Laskowski RA, Orengo CA, Thornton JM (1998)
Transactions, American Crystallographic Association, Annual Meeting 1997.
Classifying a Protein in the CATH Database of Domain Structures
Orengo, CA, Martin, AM, Hutchinson, EG, Jones, S, Jones, DT,
Michie, AD, Swindells, MB, Thornton, JM (1998)
Acta Cryst D54 p1155-1167
New Tools and Resources for Analysing Protein Structures and Their Interactions
Luscombe, NM, Laskowski, RA, Westhead, DR, Milburn, D, Jones, S, Karmirantzou M, Thornton, JM. (1998)
Acta Cryst D54 p1132-1138.
Protein Folds and Function
Martin, ACR, Orengo, CA, Hutchinson, EG, Jones, S, Laskowski, RA, Mitchell, JBO, Taroni, C, Thornton, JM (1998)
Structure, 1998, Vol 6. p.875-884.
Domain Assignment for Protein Structures using a Consensus Approach:
Characterisation and Analysis
Jones, S., Stewart, M., Michie, A., Swindells, M., Orengo, C., Thornton, J. (1998)
Protein Science Vol 7. p.233-242.
CATH- A Hierarchic Classification of Protein Domain Structures
Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M., and Thornton, J. (1997)
Structure. Vol 5. No 8. p.1093-1108
Prediction of Protein-Protein Interaction Sites Using Patch Analysis
Jones, S. and Thornton, J.M. (1997)
Journal of Molecular Biology. Vol 272 p133-143.
Analysis of Protein-Protein Interaction Sites Using Surface Patches
Jones, S. and and Thornton, J.M. (1997)
Journal of Molecular Biology. Vol 272 p121-132.
Principles of Protein-Protein Interactions Derived From Structural
Studies
Jones, S. and Thornton, J.M. (1996)
Proceedings of The National Academy of Science (U.S.A). Vol. 93 p.13-20.
Protein-Protein Interactions: A Review of Protein Dimer Structures
Jones, S. and Thornton, J.M. (1995)
In Progress in Biophysics and Molecular Biology: Vol 63 p31-165.
Updated 21/08/09
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