I collaborated in the development of Bio3d, an R package for the exploratory analysis of structure and sequence data [1].
The package contains utilities for the analysis of protein structure, sequence and molecular dynamics trajectory data. Among the implemented methods is the comparative analysis of protein structures with Principal Component Analysis. PCA facilitates the characterization of internal conformational differences and inter-conformer relationships, thus providing a framework for the analysis of protein structure evolution.
The Bio3d package is distributed with full source code as a platform independent R package under a GPL2 license from http://mccammon.ucsd.edu/~bgrant/bio3d/.
A number of structural genomics programmes have been established worldwide with the common aim of large-scale, high-throughput protein structure determination. Experimental structure determination methods are still considerably challenging, thus it is important to select and prioritise candidate molecules that will maximise the information gained from each new structure [1].
I developed sgTarget, an informatics resource capable of performing target selection through the implementation of a number of sequence analysis protocols [2,3]. The system enables structural biologists to select targets from their genomic sequences of interest, according to their research needs.
sgTarget has been successfully applied in both the EU funded Structural Proteomics IN Europe, and the Wellcome Trust funded Plasmodium Functional Genomics Initiative [4].
The resource is now publicly available at http://www.ysbl.york.ac.uk/sgTarget/.
Recently, I collaborated in the establishment of two novel feasibility scores for selecting targets likely to surpass the major bottlenecks of the structure determination pipeline: protein production and protein crystallization [5]. My contributions included an investigation into the effect of amino acid insertions on a protein's likelihood to crystallize.
Both scores are now being successfully employed in the latest rounds of target selection at the NIH funded Joint Center for Structural Genomics (part of the NIGMS Protein Structure Initiative).
Development of an NT-BLAST Cluster
With Mr. Daniel Oskarsson (Bioinformatics Group, deCODE Genetics, Iceland, 2000)
The deCODE Genetics BLAST service was modified and adapted to run large numbers of BLAST queries in a distributed fashion, using the processing power of idle desktop PCs (à la SETI@home).
Mapping the Protein Universe via Structural Alignment
With Drs. Thomas Oldfield & Leo Caves (Department of Chemistry, University of York, UK, 2000)
A novel algorithm capable of classifying proteins based on their structural characteristics was refined and evaluated using a number of multivariate statistics techniques and molecular graphics packages.
Identification of the Selenocysteinyl Elongation Factor in Eukaryotes
With Prof. Sandra Baldauf (Department of Biology, University of York, UK, 1999)
A putative selenocysteinyl elongation factor was identified within the Caenorhabditis elegans genome, through the use of sequence analysis techniques, such as database searching, multiple sequence alignment and phylogenetic analysis.
Pattern Analysis of the Moss Physcomitrella patens
With Prof. David Cove (Department of Biology, University of Leeds, UK, 1999)
A numerical description of the wild type's developmental branching pattern was established in order to allow the visual screening of gene knockout mutants.
Updated: Monday, November 5, 2007