Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the augmen
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De novo design • Antibody design • Peptide design • Binder design • Enzyme design 2) Model-based design trRosetta-based • AlphaFold2-based • DMPfold2-based • CM-Align • MSA transformer-based • DeepAb-based • TRFold2-based • GPT-based • ESM-based • Ant...
Hallucination中看似简单的改动,就完成了自洽地生成蛋白结构和对应的序列,达到无中生有的境界,最后作者也提出了鲜明的观点,Hallucination+trDesign的设计方式完全可以来解决功能片段的融合设计问题,潜在的应用场景是酶设计、金属结合蛋白,以及蛋白binder设计,也是下一章节的主要内容。 3trDesign-Motif 文献参考:Tischer D, ...
就像是在protein binder design的时候,target sequence是已知的。 decoding的时候可以跳过一些已经fix的地方,并且在decode剩下的位置的过程中将这些已经fix住的地方作为context来生成。 对于multi-chain,将per chain的relative positional encoding包括前后32个residues,并且增加了binary feature来指定interacting的pair residues...
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1–5. Here we describe a general solution to this problem that starts
Protein design and engineering are evolving at an unprecedented pace leveraging the advances in deep learning. Current models nonetheless cannot natively consider non-protein entities within the design process. Here, we introduce a deep learning approach based solely on a geometric transformer of atomic...
Fig. 1: Design strategy for building switchable oligomers. a, The two-state nature of the MWC model in the case of tetrameric haemoglobin, involves an equilibrium between two defined oligomeric states in which the monomers must all adopt either the X (blue squares) or Y (blue circles) confo...
4C and D). These results suggest that HPer is capable of locating helix binding sites on protein-protein interfaces, and at the same time gives good prediction on interacting profiles for the potential α-helix ligand binding, which is important for de novo single helix binder design. 3.4. ...
The idea of designer isopeptide bonds within a protein, and better still, between a native target protein and a de novo binder is cool, but rather unfeasible as the risks for failure are high, other technologies could conceivably achieve somewhat similar results, and there are too many technical...