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Instructor: Konstantin Popov (

Meeting Dates: 02/15/2024 – 03/27/2024

Times: TTh 2:00PM-3:15PM

Location: TBD

BIOC 670 Syllabus

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