Physical Sciences and Mathematics Commons^™

Towards Biophysical Validation Of Constraint Modeling For Rigidity Analysis Of Proteins, Filip Jagodzinski, Ileana Streinu

Computer Science: Faculty Publications

Proteins are dynamic molecules, and understanding how they flex and bend provides fundamental insights to their functions. Methods such as molecular dynamics are computationally expensive, and can simulate protein motions on limited timescales. Rigidity analysis is an alternative method, in which a protein structure is analyzed to infer which portions of the molecule are flexible. To perform rigidity analysis, a model is first constructed in which various inter-atomic stabilizing interactions are modeled according to their strength. No detailed study has been conducted as to what is the most plausible, chemically validated modeling scheme. All previous implementations have relied on heuristics, …