Methods for Protein Structure Prediction - Fox Chase Cancer Center
Methods for Protein Structure Prediction - Fox Chase Cancer Center
Methods for Protein Structure Prediction - Fox Chase Cancer Center
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Improving <strong>Structure</strong> <strong>Prediction</strong>?<br />
•Looking further afield than we usually do <strong>for</strong> new search algorithms<br />
-- computer science<br />
-- computational geometry and robotics (e.g., CCD <strong>for</strong> loop closure; k-dops)<br />
-- mathematics (e.g., graph theory <strong>for</strong> side-chain combinatorial problem)<br />
•Modern statistical analysis<br />
-- Bayesian methods (e.g., side-chain rotamers)<br />
-- mixture and hierarchical models<br />
-- non-parametric statistics<br />
•Theoretical chemistry and biophysics<br />
-- high-level quantum mechanics<br />
-- polarizable <strong>for</strong>ce fields and solvation models<br />
-- critical analysis of X-ray data (e.g., side-chain disorder)<br />
•Industrial standards <strong>for</strong> software development<br />
-- object-oriented C++ or C# coding (e.g., MolIDE)<br />
-- easy (one-click) installation<br />
-- quality control (e.g., VisualStudio not vi/gdb debugging)<br />
-- free and easy distribution to non-profit research institutions<br />
•Rigorous benchmarking with appropriate controls (e.g., alignment, side-chain and<br />
loop benchmarks)
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