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Protein Structure Prediction and Design |
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Protein
Structure - Challenge of Prediction
Involved
researchers: Chris
Bystroff in collaboration with Mohammed
Zaki, and Shekhar
Garde
Introduction:
Prediction of protein structure is one of the most challenging
fields of bioinformatics. Protein structure is important
for various aspects of basic science and applied research
on proteins. For example, a number of “conformational” diseases,
including Alzheimer’s, Mad Cow disease, cystic fibrosis,
Parkinson’s, and Type 2 diabetes are caused by disorders
of protein structure. Professor Bystroff's cutting edge research
is going beyond currently used methods of detection of protein
homology. It is aimed at predicting protein structure ab
initio. This will help in understanding complex mechanisms
of protein folding and may lead to elucidation of various
protein pathologies.
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  Researchers
Introduction
Main
publications in Protein Structure
Online
Resources
Courses
Prof. Bystroff's
publications in
--Bioinformatics
--Crystallography
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Online resources in Protein Structure Prediction:
• I-sites
Courses: Professor Bystroff
covers protein structure prediction in several courses offered at
RPI: Sequence Analysis, Molecular Modeling, and X-ray Crystallography
Prof. Bystroff's publications in Bioinformatics:
Bystroff, C.
& Baker, D. (1997). Blind predictions of local protein structure
in CASP2 targets using the I-sites library. Proteins Suppl 1, 167-71.
Bystroff,
C. & Baker, D. (1998). Prediction of local structure in proteins
using a library of sequence-structure motifs. J Mol Biol 281, 565-77.
Bystroff, C.
& Garde, S. (2003). Helix propensitites of short peptides:
Molecular dynamics versus Bioinformatics. Proteins 50, (in press).
>>
more publications
Prof. Bystroff's publications in Crystallography:
Baker, D., Bystroff, C., Fletterick, R. J. & Agard,
D. A. (1993). PRISM: topologically constrained phase refinement for
macromolecular crystallography.
Bystroff, C. (2001). An alternative derivation of the equations of
motion in torsion space for a branched linear chain. Protein Engineering
14, 825-828.
Bystroff, C. (2003). MASKER: Improved solvent excluded molecular
surface area estimations using Boolean masks. Protein Eng (in press).
Bystroff, C., Baker, D., Fletterick, R. J. & Agard, D. A. (1993).
PRISM: application to the solution of two protein structures. Acta
Crystallographica, Section D (Biological Crystallography) D49, pt.5,
440-8.
Bystroff, C. & Kraut, J. (1991). Crystal structure of unliganded
Escherichia coli dihydrofolate reductase. Ligand-induced conformational
changes and cooperativity in binding. Biochemistry 30, 2227-39.
Bystroff, C., Oatley, S. J. & Kraut, J. (1990). Crystal structures
of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme
and the folate.NADP+ ternary complex. Substrate binding and a model
for the transition state. Biochemistry 29, 3263-77.
Goddette, D. W., Paech, C., Yang, S. S., Mielenz, J. R., Bystroff,
C., Wilke, M. E. & Fletterick, R. J. (1992). The crystal structure
of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A
resolution. J Mol Biol 228, 580-95.
McGrath, M. E., Erpel, T., Bystroff, C. & Fletterick, R. J. (1994).
Macromolecular chelation as an improved mechanism of protease inhibition:
structure of the ecotin-trypsin complex. Embo J 13, 1502-7.
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