Bits-to-Binders Resources

Resources for the BioML Challenge 2024: Bits to Binders

Table of Contents:

• Protein Design
  • Protein Structure Prediction
  • Inverse Folding
  • Generative Models
  • Encoder Models
  • Other Useful Tools
  • Relevant Literature
  • Miscellaneous
• Biology
  • CAR-T Literature
  • CD20 Literature
• Compute Resources
  • TACC
  • Other

Protein Design

Here is a compilation of many tools used by the UT Austin BioML Society. This is not a comprehensive list so we are likely missing some great tools. For a comprehensive list, check out this great repository!

Protein Structure Prediction

• AlphaFold2 / ColabFold [paper] [code] / [colab] [Docker]
• ESMFold [paper] [code] [server]
• RoseTTAFold [paper] [code]
• RoseTTAFoldAllAtom [paper] [code]
• UMol [paper] [code]
• AlphaFold2-RAVE [paper] [code]

Inverse Folding

• ProteinMPNN [paper] [repo]
• LigandMPNN [paper] [repo]
• ESM-IF1 [paper] [repo] [colab]

Generative Models

• RFDiffusion [paper] [code] [colab] [Docker]
• RFDiffusionAllAtom [paper] [code]
• Protpardelle paper code
• Chroma paper code
• ProGen [paper] [code]
• Framediff [paper] [code]
• Genie [paper] [code]
• FoldFlow [paper] [code]
• FrameFlow [paper] [code]
• Proteus [paper] [code]
• Multiflow [paper] [code]
• PepFlow [paper] [code]

Language Models

• ESM-2 [paper] [code]
• SaProt [paper] [code]
• Prost-T5 [paper] [code]
• ProtBERT paper huggingface
• ProtTrans paper code

Other Useful Tools

• FoldSeek [paper] [code] [server]
• MMseqs2 [paper] [code]
• MutCompute [paper] [server]

Relevant Literature

• Improving de novo protein binder design with deep learning, Bennett et al., 2023
• Improving Protein Expression, Stability, and Function with ProteinMPNN, Sumida et al., 2024

Miscellaneous

• Lecture on Protein Structure Prediction from the BioML Society [video] [slides]
• Lecture on Protein Design from the BioML Society [video] [slides]

Biology

CAR-T Literature

• CAR T cell immunotherapy for human cancer, June et al., 2018
• Recent advances and discoveries in the mechanisms and functions of CAR T cells, Larson et al., 2021
• CAR-T design: Elements and their synergistic function, Jayaraman et al., 2020

CD20 Literature

• The Development of a Recombinant scFv Monoclonal Antibody Targeting Canine CD20 for Use in Comparative Medicine, Jain et al., 2016
• CD20 as a target for therapy, Winiarska et al., 2007
• Mechanisms of action of CD20 antibodies, Boross et al., 2012
• Rituximab (monoclonal anti-CD20 antibody): mechanisms of action and resistance, Smith 2003

Compute Resources

TACC

• Brief Overview
• Vista Supercomputer
• Containers on TACC
• Login
• Create account

Other Compute

• Synthia - LLM that uses protein design tools
• Tools suggested by Adaptyv Bio