REECE'S RESEARCH INTERESTS Last Updated $Date: 2000/01/07 03:09:27 $
PAST AND PRESENT RESEARCH INTERESTS	Potential Smoothing (thesis work, Ph.D. Molecular Biophysics) I'm actively involved in the development of potential smoothing as a method to facilitate conformational search, demonstrations of its similarities with simulated annealing, and applications to in vacuo structure prediction, crystal structure prediction, and molecular docking. This work is the basis for my thesis and several submitted and soon-to-be-submitted papers. Automated Sequence Analysis (thesis work, Masters Computer Science) I developed a set of C++ classes for the analysis of automated DNA sequencing data, such as is generated by Applied Biosystems' products. These classes were the basis for a Bayesian peak identification model. The source code is freely available below. Protein Structure Prediction by Integrating Multiple Sources of Information Most of my time lately is focusing on forming postdoc projects ideas, with particular emphasis on protein structure prediction by incorporating information from homology modeling, threading, secondary structure prediction, empirical force fields, and other methods. My goal is a postdoc with these issues in mind and an eye toward future CASP events. Computational Biology Algorithms and Software Development I'm very interested in software design issues, and particularly how design choices influence the accessibility and flexibility of software from the end users' perspectives. Software may be designed with accessibility (interfaces) on several levels: source code, link-time libraries, dynamically loaded libraries, scripting languages (e.g., perl, python, tcl/tk), command line, and graphical user interfaces. Modern development tools and techniques frequently allow broad accessibility with only moderate additional coding. This issue is especially relevant in rapidly changing research software where multiple levels of accessibility are needed for rapid prototyping, but is hindered by the difficulty of keeping multiple interfaces consistent with the underlying code.
URL: http://www.in-machina.com/~reece/research.html Last Updated: $Date: 2000/01/07 03:09:27 $ keywords: biophysics, potential smoothing, molecular modelling, perl, autoseq, rasmol maintainer: Reece Hart <reece@in-machina.com> [ home page | send mail ]