Abstract
This April, in Cambridge (UK), principal investigators from the Mathematical Biology Group of the Medical Research Council's National Institute of Medical Research organized a workshop in structural bioinformatics at the Centre for Mathematical Sciences. Bioinformatics researchers of several nationalities from labs around the country presented and discussed their computational work in biomolecular structure prediction and analysis, and in protein evolution. The meeting was intensive and lively and gave attendees an overview of the healthy state of protein bioinformatics in the UK.
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Selected References
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- Burke D. F., Deane C. M. Improved protein loop prediction from sequence alone. Protein Eng. 2001 Jul;14(7):473–478. doi: 10.1093/protein/14.7.473. [DOI] [PubMed] [Google Scholar]
- Calladine C. R., Sharff A., Luisi B. How to untwist an alpha-helix: structural principles of an alpha-helical barrel. J Mol Biol. 2001 Jan 19;305(3):603–618. doi: 10.1006/jmbi.2000.4320. [DOI] [PubMed] [Google Scholar]
- Cavallo Luigi, Kleinjung Jens, Fraternali Franca. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res. 2003 Jul 1;31(13):3364–3366. doi: 10.1093/nar/gkg601. [DOI] [PMC free article] [PubMed] [Google Scholar]
- DePristo Mark A., de Bakker Paul I. W., Blundell Tom L. Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure. 2004 May;12(5):831–838. doi: 10.1016/j.str.2004.02.031. [DOI] [PubMed] [Google Scholar]
- DePristo Mark A., de Bakker Paul I. W., Lovell Simon C., Blundell Tom L. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins. 2003 Apr 1;51(1):41–55. doi: 10.1002/prot.10285. [DOI] [PubMed] [Google Scholar]
- Fernández-Recio Juan, Totrov Maxim, Abagyan Ruben. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol. 2004 Jan 16;335(3):843–865. doi: 10.1016/j.jmb.2003.10.069. [DOI] [PubMed] [Google Scholar]
- Fraternali Franca, Cavallo Luigi. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res. 2002 Jul 1;30(13):2950–2960. doi: 10.1093/nar/gkf373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johannissen Linus O., Taylor William R. Protein fold comparison by the alignment of topological strings. Protein Eng. 2003 Dec;16(12):949–955. doi: 10.1093/protein/gzg128. [DOI] [PubMed] [Google Scholar]
- Jones Susan, Shanahan Hugh P., Berman Helen M., Thornton Janet M. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res. 2003 Dec 15;31(24):7189–7198. doi: 10.1093/nar/gkg922. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Laskowski Roman A., Watson James D., Thornton Janet M. From protein structure to biochemical function? J Struct Funct Genomics. 2003;4(2-3):167–177. doi: 10.1023/a:1026127927612. [DOI] [PubMed] [Google Scholar]
- Lin Kuang, Kleinjung Jens, Taylor William R., Heringa Jaap. Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. Comput Biol Chem. 2003 May;27(2):93–102. doi: 10.1016/s1476-9271(03)00022-7. [DOI] [PubMed] [Google Scholar]
- Lindorff-Larsen Kresten, Kristjansdottir Sigridur, Teilum Kaare, Fieber Wolfgang, Dobson Christopher M., Poulsen Flemming M., Vendruscolo Michele. Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein. J Am Chem Soc. 2004 Mar 17;126(10):3291–3299. doi: 10.1021/ja039250g. [DOI] [PubMed] [Google Scholar]
- Madera Martin, Vogel Christine, Kummerfeld Sarah K., Chothia Cyrus, Gough Julian. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D235–D239. doi: 10.1093/nar/gkh117. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shi J., Blundell T. L., Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. 2001 Jun 29;310(1):243–257. doi: 10.1006/jmbi.2001.4762. [DOI] [PubMed] [Google Scholar]
- Shirai H., Blundell T. L., Mizuguchi K. A novel superfamily of enzymes that catalyze the modification of guanidino groups. Trends Biochem Sci. 2001 Aug;26(8):465–468. doi: 10.1016/s0968-0004(01)01906-5. [DOI] [PubMed] [Google Scholar]
- Shirai Hiroki, Mizuguchi Kenji. Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism. FEBS Lett. 2003 Dec 18;555(3):505–510. doi: 10.1016/s0014-5793(03)01314-0. [DOI] [PubMed] [Google Scholar]
- Stebbings Lucy A., Mizuguchi Kenji. HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D203–D207. doi: 10.1093/nar/gkh027. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Taylor W. R. A deeply knotted protein structure and how it might fold. Nature. 2000 Aug 24;406(6798):916–919. doi: 10.1038/35022623. [DOI] [PubMed] [Google Scholar]
- Taylor William R. A 'periodic table' for protein structures. Nature. 2002 Apr 11;416(6881):657–660. doi: 10.1038/416657a. [DOI] [PubMed] [Google Scholar]
- Taylor William R. A 'periodic table' for protein structures. Nature. 2002 Apr 11;416(6881):657–660. doi: 10.1038/416657a. [DOI] [PubMed] [Google Scholar]
- Ward J. J., Sodhi J. S., McGuffin L. J., Buxton B. F., Jones D. T. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol. 2004 Mar 26;337(3):635–645. doi: 10.1016/j.jmb.2004.02.002. [DOI] [PubMed] [Google Scholar]
- de Bakker Paul I. W., DePristo Mark A., Burke David F., Blundell Tom L. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins. 2003 Apr 1;51(1):21–40. doi: 10.1002/prot.10235. [DOI] [PubMed] [Google Scholar]
