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
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...
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 ...
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...
Attemptstorationallydesignligand-bindingproteinshavemetwith littlesuccess,however,andthecomputationaldesignofprotein– small-moleculeinterfacesremainsanunsolvedproblem 1 .Current approachesfordesigningligand-bindingproteinsformedical 2 and biotechnologicalusesrelyonraisingantibodiesagainstatarget ...
Design of ligand binding proteins faces several challenges including sampling of the enormous possible orientations of the ligand with respect to the protein, the large conformational and the sequence space of the protein pocket, and the difficulties in accurately estimating the binding free energies ...
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,...
Since then, dramatic advances have taken place in the methodology of peptide and protein chemistry, as well as molecular biology, that have led to a vastly improved understanding of the complex interplay among sequential, structural, and functional properties of natural proteins (2–5). With the ...
- 《Proteins Structure Function & Bioinformatics》 被引量: 156发表: 2003年 Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions Many drugs, even ones that are designed to act selectively on a target protein, bind unintended ...
Evidence from in vivo studies suggests that tension on the ECM protein fibronectin triggers domain unfolding exposing cryptic binding sites that are important for the ECM assembly (Ohashi et al., 1999). The physical properties underlying the mechanical functions of proteins are largely unknown, but ...