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 challenge1,2,3,4,5. Here we describe a general solution to this problem that starts with a broad exploration of th...
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 augmentation of energy-based protein binder design ...
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 an outstanding challenge. We describe a general solution to this problem which starts with a broad exploration of the very...
protein designnatural scaffoldsdesign of enzymesdesign of binding proteinsaltered alphabetsde novoSummary This chapter contains sections titled: Introduction Design of Proteins from Natural Scaffolds Design of Enzymes Grafting Catalytic Sites in Proteins Endowing Enzymes with Two Catalytic Activities in a ...
protein designnatural scaffoldsdesign of enzymesdesign of binding proteinsaltered alphabetsde novoDegeneracy in the genetic code is known to minimise the deleterious effects of the most frequent base substitutions: transitions at the third base of codons are generally synonymous substitutions. Transversions...
8 Theabilitytodesignproteinswithhighaffinityandselectivityfor anygivensmallmoleculeisarigoroustestofourunderstandingof thephysiochemicalprinciplesthatgovernmolecularrecognition. Attemptstorationallydesignligand-bindingproteinshavemetwith littlesuccess,however,andthecomputationaldesignofprotein– small-moleculeinterfacesremainsan...
Protein CREATE enables closed-loop design of de novo synthetic protein binders [bioRxiv 2024.12.20.629847] • ESM-IF-based Implicit modeling of the conformational landscape and sequence allows scoring and generation of stable proteins [bioRxiv 2024.12.20.629706] • [code] • [Supplementary]...
文献参考:Tischer D, Lisanza S, Wang J, et al. Design of proteins presenting discontinuous functional sites using deep learning[J]. bioRxiv, 2020. 在2020年末的11月,千呼万唤的融合功能Motif的设计方法出来了,其中主要的工作贡献是将trDesign和Hallucination有机的结合起来。具体的核心思想在于分而治之,...
of protein sequences. The methods described here present one approach to distill the general principles, if any, for the design of natural proteins. Practically, such rules might permit the design of improved synthetic proteins that show natural-like properties of highcatalytic efficiency, mutational...
Deeper investigations of protein-protein interfaces relevant to human oncogenesis and cancer-associated protein-protein interaction networks have shown that cancer-related proteins are smaller, more planar, more charged, and less hydrophobic binding sites than non-cancer-related proteins and they tend to...