BIOC 670 Structural Bioinformatics
Instructor: Konstantin Popov (firstname.lastname@example.org)
Meeting Dates: 01/09/2023 – 02/10/2023
Times: TTh 9:30AM-10:45AM
Location: GMB 3007
This module will introduce modern methods and techniques for protein structure prediction and analysis. Techniques that will be covered include homology modeling, de novo structure prediction, protein-protein and protein-ligand docking, and protein design. It will consist of nine lectures (1.5 h each), homework assignments and an exam.
Computational Structural Biology
- Algorithms for sequence optimization
- Energy functions for protein design
- Integration of experimental and computational techniques in structural genomics projects. Protein Data Bank. Overview of experimental structure determination: NMR, X-ray crystallography.
- The taxonomy of protein structure. Algorithms for structure comparison and fold classification schemes.
- Empirical and statistical macromolecular force fields for structure simulation and prediction.
- The complexity of the protein folding problem; Protein folding simulations.
- Knowledge-Based Protein Homology Modeling. Sequence alignment in the context of structure prediction.
- Fold recognition approach to structure prediction. The ongoing challenge on Critical Assessment of Structure Prediction (CASP): Successes and failures.
- Protein design and stability.
- The relationship between protein structure and function. Computational structural genomics approaches to function prediction.
- Computational Approaches to Structure-Based Drug Design: Methods and Applications.
Homology modeling (predicting structure based on the structure of a related protein)
- Fold recognition
- Sequence alignments in the context of structure prediction
- Loop modeling / refining low-resolution models
De novo structure prediction (predicting protein structures from scratch)
- Real-time protein folding simulations / Molecular Dynamics and Monte Carlo
- Knowledge based approaches/ Rosetta
- Machine Learning based approaches/ AlphaFold
Protein – protein docking
- Search protocols
- Scoring functions
Protein – ligand docking
- Protein binding site identification
- Scoring functions
- Conformational sampling algorithmes