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Updated: Aug 2, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Geometric analysis of cross-linkability for protein fold discrimination
S Potluri1, A A Khan, A Kuzminykh
1Dept of Comp. Sci., Purdue Univ., West Lafayette, IN 47907, USA.
Abstract:
Protein structure provides insight into the evolutionary origins, functions, and mechanisms of proteins. We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, high-throughput experiments. One such experiment is residue-specific cross-linking analyzed by mass spectrometry. This paper presents a suite of novel lower- and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking results. Through analysis and computational experiments, using simulated and published experimental data, we demonstrate that our algorithms enable effective model discrimination.
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