Playlist: https://tinyurl.com/MLCBlectures
Notes: https://tinyurl.com/MLCB24notes
Lecture Slides: https://www.dropbox.com/scl/fi/b5c3g8f6suhukr7gurn9m/Lecture09_10_AlgorithmsForProteinStructure.pdf?rlkey=7pae9yyet12rnqi4daongwnf6&dl=0
Lecture Chapter: https://www.dropbox.com/scl/fi/n55sk5jf8bsb5b91vfzue/Lecture10_AlgorithmsForProteinStructure.pdf?rlkey=hwluckc4s71vybfmmsjuc4bea&dl=0
00:00 Algorithms for protein structure using transformers
4:30 AlphaFold 3 architecture changes
7:50 Protein design
14:05 Diffusion models
19:00 Protein Language Models (PLMs)
24:30 Encoder-Decoder architectures
34:35 Limitations of encoder-decoder, and the transformer
49:20 Tokenization, semantic embedding, positional embedding
55:00 Information flow in a transformer and normalization
59:30 Attention mechanism
1:13:50 Residual connections
1:17:18 Comparison with other models
