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Course10610523062 lectures

Algorithms for protein modelling and engineering

Prof. Pralay Mitra · IIT Kharagpur

Start with lecture 1 At NPTEL

Lectures

week-01

  1. Lecture 01: Introduction on Proteins Video
  2. Lecture 02: Introduction on Proteins (Contd.) and Sequence Database Video
  3. Lecture 03: Protein Data Bank Video
  4. Lecture 04: PDB Parsing Video
  5. Lecture 05: Molecular Visualization Tools Video

week-02

  1. Lecture 06: Representation and Data Structure Video
  2. Lecture 07: Digitization of a Molecule Video
  3. Lecture 08: Application to Protein Docking, FFT Video
  4. Lecture 09: Implementation Details Video
  5. Lecture 10: Hashing Video

week-03

  1. Lecture 11: Geometric Hashing Video
  2. Lecture 12: Geometric Hashing (Contd.) Video
  3. Lecture 13: Geometric Hashing (Contd.) Video
  4. Lecture 14: Molecular Surface Video
  5. Lecture 15: Genetic Algorithm (GA) for Surface Comparison Video

week-04

  1. Lecture 16: Monte Carlo (MC) Method Video
  2. Lecture 17: Monte Carlo Method (Contd.) and Random Number Video
  3. Lecture 18: Monte Carlo (MC) Method (Contd.) Video
  4. Lecture 19: Protein Folding Video
  5. Lecture 20: Protein Folding (Contd.) and Protein Design Video

week-05

  1. Lecture 21: Protein Energy Landscape Video
  2. Lecture 22: Protein Energy Landscape (Contd.), Limitation of MC Video
  3. Lecture 23: Replica Exchange Monte Carlo (REMC) Video
  4. Lecture 24: Ab Initio Protein Folding Video
  5. Lecture 25: Structure Alignment Measures Video

week-06

  1. Lecture 26: Dynamic Programming Video
  2. Lecture 27: Dynamic Programming (Contd.), Sequence Alignment Video
  3. Lecture 28: Dynamic Programming (Contd.), Position Specific Scoring Matrix (PSSM) Video
  4. Lecture 29: Structure Alignment Video
  5. Lecture 30: Structure Alignment (Contd.) Video

week-07

  1. Lecture 31: Structural Classification of Proteins (SCOP) Video
  2. Lecture 32: SCOP (Contd.), Symmetry in Proteins Video
  3. Lecture 33: Symmetry in Proteins Video
  4. Lecture 34: Discriminating Biological Protein Interfaces from Crystal Artifacts Video
  5. Lecture 35: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.) Video

week-08

  1. Lecture 36: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.) Video
  2. Lecture 37: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.) Video
  3. Lecture 38: Symmetry-Based Protein Complex Modeling Video
  4. Lecture 39: Some Protein Docking Methods Video
  5. Lecture 40: Some Protein Docking Methods (Contd.) Video

week-09

  1. Lecture 41: Computational Protein Design (CPD) Video
  2. Lecture 42: Computational Protein Design (CPD) (Contd.) Video
  3. Lecture 43: Protein Design Energy Function Video
  4. Lecture 44: Protein Design Analysis Video
  5. Lecture 45: Application of Protein Design on Drug Design Video

week-10

  1. Lecture 46: RECM in Protein Design Video
  2. Lecture 47: Application of Protein Design on Drug Design Video
  3. Lecture 48: Application of Protein Design on Drug Design (Contd.), Protein Modification Video
  4. Lecture 49: Protein Modification (Contd.) Video
  5. Lecture 50: Protein Modification (Contd.) Video

week-11

  1. Lecture 51: Assigning Secondary Structure to Protein Sequence Video
  2. Lecture 52: Assigning Secondary Structure to Protein Sequence (Contd.) Video
  3. Lecture 53: Machine Learning to Predict the Secondary Structure from Amino Acid Sequences Video
  4. Lecture 54: Machine Learning to Predict the Secondary Structure from Amino Acid Sequences (Contd.) Video
  5. Lecture 55: Post Translational Modification Video

week-12

  1. Lecture 56: Predicting Protein Phosphorylation Sites Video
  2. Lecture 57: Predicting Protein Phosphorylation Sites (Contd.) Video
  3. Lecture 58: Summarizing Protein Folding and Protein Docking Video
  4. Lecture 59: Summarizing Protein Folding and Protein Docking (Contd.) Video
  5. Lecture 60: Summarizing Potein Engineering Video

Live Session

  1. Live Session 09-08-2021 Video
  2. Live Session 06-10-2021 Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IIT Kharagpur
Department
Computer Science and Engineering
Teacher
Prof. Pralay Mitra
Level
Undergraduate
Language
English
Subjects
Computer science, Engineering
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
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