Protein Modeling in Bioinformatics: Ab Initio, Energy-Based, and Knowledge-Based Methods -, Study notes of Bioinformatics

Download Protein Modeling in Bioinformatics: Ab Initio, Energy-Based, and Knowledge-Based Methods - and more Study notes Bioinformatics in PDF only on Docsity! Iosif Vaisman Email: ivaisman@gmu.edu Introduction to Bioinformatics Protein Modeling Methods • Ab initio methods: solution of a protein folding problem search in conformational space • Energy-based methods: energy minimization molecular simulation • Knowledge-based methods: homology modeling fold recogniion a pattern that exceeds certain threshold of interestingness. Knowledge Knowledge is ... Factors that contribute to interestingness: coverage confidence statistical significance simplicity unexpectedness actionability Knowledge-based methods Finding patterns in known structures Deriving rules (usually in the form of PMF) Applying the rules Protein representation (Crambin) Protein representation (Crambin) 4 neighbors 7 neighbors 2 neighbors 10 neighbors Neighbor identification in proteins Voronoi Tessellation Delaunay simplex is defined by points, whose Voronoi polyhedra have common vertex Delaunay simplex is always a triangle in a 2D space and a tetrahedron in a 3D space Delaunay Tessellation Neighbor identification in proteins: Voronoi/Delaunay Tessellation in 2D Neighbor identification in proteins: Voronoi/Delaunay Tessellation in 2D Voronoi Tessellation Delaunay Tessellation Neighbor identification in proteins: Voronoi/Delaunay Tessellation in 2D 6 7 6 Delaunay tessellation of Crambin Delaunay tessellation of Crambin