# Algorithms for protein modelling and engineering

- Institution: IIT Kharagpur
- Department: Computer Science and Engineering
- Teacher: Prof. Pralay Mitra
- Level: Undergraduate
- Language: English
- Subjects: Computer science, Engineering
- Source: [NPTEL](https://nptel.ac.in/courses/106105230)
- Licence: [CC BY-NC-SA](https://nptel.ac.in/faq) (Non-commercial use only.)
- Syllabus: [at the source](https://nptel.ac.in/courses/106105230)
- Who can watch: Teens profiles and older (sources give no ratings; placed by Invisible Network from the source's own words)

## Lectures

1. [Lecture 01: Introduction on Proteins](https://invisiblenetwork.ai/learn/nptel/106105230/3fb1f3df4627) (Video)
2. [Lecture 02: Introduction on Proteins (Contd.) and Sequence Database](https://invisiblenetwork.ai/learn/nptel/106105230/cd6122675625) (Video)
3. [Lecture 03: Protein Data Bank](https://invisiblenetwork.ai/learn/nptel/106105230/5d7be616c781) (Video)
4. [Lecture 04: PDB Parsing](https://invisiblenetwork.ai/learn/nptel/106105230/0963f56000b5) (Video)
5. [Lecture 05: Molecular Visualization Tools](https://invisiblenetwork.ai/learn/nptel/106105230/31b7bfcbc263) (Video)
6. [Lecture 06: Representation and Data Structure](https://invisiblenetwork.ai/learn/nptel/106105230/bc7867b2a926) (Video)
7. [Lecture 07: Digitization of a Molecule](https://invisiblenetwork.ai/learn/nptel/106105230/4cecbd8d0c43) (Video)
8. [Lecture 08: Application to Protein Docking, FFT](https://invisiblenetwork.ai/learn/nptel/106105230/c76728f076f5) (Video)
9. [Lecture 09: Implementation Details](https://invisiblenetwork.ai/learn/nptel/106105230/00eeb97a5fb9) (Video)
10. [Lecture 10: Hashing](https://invisiblenetwork.ai/learn/nptel/106105230/fb52dbc56ca0) (Video)
11. [Lecture 11: Geometric Hashing](https://invisiblenetwork.ai/learn/nptel/106105230/dddc2460b58b) (Video)
12. [Lecture 12: Geometric Hashing (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/d6f59cd63a0d) (Video)
13. [Lecture 13: Geometric Hashing (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/2c3fb4242f93) (Video)
14. [Lecture 14: Molecular Surface](https://invisiblenetwork.ai/learn/nptel/106105230/7821ea6ff2b5) (Video)
15. [Lecture 15: Genetic Algorithm (GA) for Surface Comparison](https://invisiblenetwork.ai/learn/nptel/106105230/0b58f07db5e5) (Video)
16. [Lecture 16: Monte Carlo (MC) Method](https://invisiblenetwork.ai/learn/nptel/106105230/abba5d96ab2b) (Video)
17. [Lecture 17: Monte Carlo Method (Contd.) and Random Number](https://invisiblenetwork.ai/learn/nptel/106105230/94d90457a53f) (Video)
18. [Lecture 18: Monte Carlo (MC) Method (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/e58adf468965) (Video)
19. [Lecture 19: Protein Folding](https://invisiblenetwork.ai/learn/nptel/106105230/9ecb02795da7) (Video)
20. [Lecture 20: Protein Folding (Contd.) and Protein Design](https://invisiblenetwork.ai/learn/nptel/106105230/792b98b1518e) (Video)
21. [Lecture 21: Protein Energy Landscape](https://invisiblenetwork.ai/learn/nptel/106105230/0894a7885daf) (Video)
22. [Lecture 22: Protein Energy Landscape (Contd.), Limitation of MC](https://invisiblenetwork.ai/learn/nptel/106105230/172585789eaa) (Video)
23. [Lecture 23: Replica Exchange Monte Carlo (REMC)](https://invisiblenetwork.ai/learn/nptel/106105230/c6341b3bd035) (Video)
24. [Lecture 24: Ab Initio Protein Folding](https://invisiblenetwork.ai/learn/nptel/106105230/41261cf97301) (Video)
25. [Lecture 25: Structure Alignment Measures](https://invisiblenetwork.ai/learn/nptel/106105230/39f9400168bd) (Video)
26. [Lecture 26: Dynamic Programming](https://invisiblenetwork.ai/learn/nptel/106105230/e1c0a5e00108) (Video)
27. [Lecture 27: Dynamic Programming (Contd.), Sequence Alignment](https://invisiblenetwork.ai/learn/nptel/106105230/8ad24301cf53) (Video)
28. [Lecture 28: Dynamic Programming (Contd.), Position Specific Scoring Matrix (PSSM)](https://invisiblenetwork.ai/learn/nptel/106105230/dfa493a1bfb9) (Video)
29. [Lecture 29: Structure Alignment](https://invisiblenetwork.ai/learn/nptel/106105230/ccf319b552d8) (Video)
30. [Lecture 30: Structure Alignment (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/2e85689c92ab) (Video)
31. [Lecture 31: Structural Classification of Proteins (SCOP)](https://invisiblenetwork.ai/learn/nptel/106105230/4236cd26b9c1) (Video)
32. [Lecture 32: SCOP (Contd.), Symmetry in Proteins](https://invisiblenetwork.ai/learn/nptel/106105230/016fee1fa382) (Video)
33. [Lecture 33: Symmetry in Proteins](https://invisiblenetwork.ai/learn/nptel/106105230/a4195f897f48) (Video)
34. [Lecture 34: Discriminating Biological Protein Interfaces from Crystal Artifacts](https://invisiblenetwork.ai/learn/nptel/106105230/43e7428bd7e6) (Video)
35. [Lecture 35: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/927a0a12bf57) (Video)
36. [Lecture 36: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/2f0e1df5330e) (Video)
37. [Lecture 37: Discriminating Biological Protein Interfaces from Crystal Artifacts (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/0508f1fec29f) (Video)
38. [Lecture 38: Symmetry-Based Protein Complex Modeling](https://invisiblenetwork.ai/learn/nptel/106105230/2c8cbd068e40) (Video)
39. [Lecture 39: Some Protein Docking Methods](https://invisiblenetwork.ai/learn/nptel/106105230/71a262f3038b) (Video)
40. [Lecture 40: Some Protein Docking Methods (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/0824d39d4984) (Video)
41. [Lecture 41: Computational Protein Design (CPD)](https://invisiblenetwork.ai/learn/nptel/106105230/f190742d35cc) (Video)
42. [Lecture 42: Computational Protein Design (CPD) (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/490a37d18b71) (Video)
43. [Lecture 43: Protein Design Energy Function](https://invisiblenetwork.ai/learn/nptel/106105230/4fa51d0bf740) (Video)
44. [Lecture 44: Protein Design Analysis](https://invisiblenetwork.ai/learn/nptel/106105230/5e563a2a49ca) (Video)
45. [Lecture 45: Application of Protein Design on Drug Design](https://invisiblenetwork.ai/learn/nptel/106105230/ef4896ee4c07) (Video)
46. [Lecture 46: RECM in Protein Design](https://invisiblenetwork.ai/learn/nptel/106105230/731088edb024) (Video)
47. [Lecture 47: Application of Protein Design on Drug Design](https://invisiblenetwork.ai/learn/nptel/106105230/b2347e4d502a) (Video)
48. [Lecture 48: Application of Protein Design on Drug Design (Contd.), Protein Modification](https://invisiblenetwork.ai/learn/nptel/106105230/9f8a00459b86) (Video)
49. [Lecture 49: Protein Modification (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/dabe952c5cc8) (Video)
50. [Lecture 50: Protein Modification (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/86d42b425120) (Video)
51. [Lecture 51: Assigning Secondary Structure to Protein Sequence](https://invisiblenetwork.ai/learn/nptel/106105230/767b567d1a92) (Video)
52. [Lecture 52: Assigning Secondary Structure to Protein Sequence (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/68cb09e2ca08) (Video)
53. [Lecture 53: Machine Learning to Predict the Secondary Structure from Amino Acid Sequences](https://invisiblenetwork.ai/learn/nptel/106105230/f21a561c45c3) (Video)
54. [Lecture 54: Machine Learning to Predict the Secondary Structure from Amino Acid Sequences (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/76235c62c511) (Video)
55. [Lecture 55: Post Translational Modification](https://invisiblenetwork.ai/learn/nptel/106105230/bfaec7c3b6a8) (Video)
56. [Lecture 56: Predicting Protein Phosphorylation Sites](https://invisiblenetwork.ai/learn/nptel/106105230/c019db5976cd) (Video)
57. [Lecture 57: Predicting Protein Phosphorylation Sites (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/e61bd0d83152) (Video)
58. [Lecture 58: Summarizing Protein Folding and Protein Docking](https://invisiblenetwork.ai/learn/nptel/106105230/aea542198e45) (Video)
59. [Lecture 59: Summarizing Protein Folding and Protein Docking (Contd.)](https://invisiblenetwork.ai/learn/nptel/106105230/23bc30ae4aed) (Video)
60. [Lecture 60: Summarizing Potein Engineering](https://invisiblenetwork.ai/learn/nptel/106105230/77645e561a68) (Video)
61. [Live Session 09-08-2021](https://invisiblenetwork.ai/learn/nptel/106105230/3fb1f3df4627-2) (Video)
62. [Live Session 06-10-2021](https://invisiblenetwork.ai/learn/nptel/106105230/cd6122675625-2) (Video)