Projects sharing features with Af2seq

Fold-conditioned de novo binder design FoldCraft enables fold-conditioning of binder structure, enabling design of binders with diverse folds like TIM-barrels, solenoid folds or Ig-like domains. Using VHH conditioned framework FoldCraft can succesfully design single domain nanobody binders…

Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. Select your target and let the script do the rest of the work and finish once you have enough designs to order!

HalluDesign, a hallucination-driven all-atom framework for the iterative co-optimization and co-design of protein sequences and structures by leveraging the forward pass of a structure prediction model

In silico directed evolution of peptide binders \ \ EvoBind (v2) designs novel peptide binders based only on a protein target sequence. It is not necessary to specify any target residues within the protein sequence or the length of the binder (although this is possible). Cyclic binder design is…

Modelling of Large Protein Complexes version 1.0

Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.

P(structure | sequence) - TrDesign - using TrRosetta for design - AfDesign - using AlphaFold for design - WIP RfDesign - using RoseTTAFold for design - P(sequence | structure) - ProteinMPNN - WIP TrMRF - P(sequence) - WIP MSA_transformer - WIP SEQ - (GREMLIN, mfDCA, arDCA, plmDCA, bmDCA,…

Source code to accompany: End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman See: https://www.biorxiv.org/content/10.1101/2021.10.23.465204v1

Scripts for predicting how short fragments of natural proteins bind to full-length proteins, as described in the manuscript. This program is built on top of MMseqs2 and ColabFold, extending them to efficiently predict interactions between a full-length protein and fragments derived from a protein.

ColabFold on your local PC (or macOS). See also ColabFold repository.

Automated protein backbone refinement from a protein sketch as described in: