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...
Cell-free genetically encoded biosensors have been developed to detect small molecules and nucleic acids, but they have yet to be reliably engineered to detect proteins. Here we develop an automated platform to convert protein-binding RNA aptamers into r
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 ...
The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predic... K Tomasz,DT Jones,CM Deane - 《Plos One》 被引量: 117发表: 2014年 De novo prediction of DNA-binding specificities for Cys2His2 zinc...
作者称之为RFjoint。RFjoint的在测试集denovo protein设计任务上的的sequence recovery达到33%,与Rosetta FastDesign类似。 为了验证RFjoint对结构的补全能力,作者选取了2KL8晶体结构中的小段区域来进行mask,试图让RFjoint来补全这段结构的同时预测他的序列,从目前的结果来看,RFjoint完全可以胜任此任务,作者也在更多的...
putationalmethodfordesigningpre-organizedandshapecomple- mentarysmall-molecule-bindingsites,anduseittogenerateprotein binderstothesteroiddigoxigenin(DIG).Ofseventeenexperimentally characterizeddesigns,twobindDIG;themodelofthehigheraffinity binderhasthemostenergeticallyfavourableandpre-organizedinter- faceinthedesignset....
It provides highly accurate predictions of protein 3D structures PDBbind PDBbind is a comprehensive collection of the binding data of all types of biomolecular complexes in the PDB database. It is primarily used for the development and validation of computational methods for predicting molecular ...
Template-based design of protein–protein interactions 基于模板的方法包括将现有PPI的结合基序移植到新的结构环境中(图2)。该基序通过侧链移植(即模仿主链然后替换侧链)或主链移植(即包括侧链和主链的全基序移植)移植到蛋白质支架上。或者,可以围绕该结合基序构建从头蛋白支架。 Figure 2. PPI design methods using ...
Protein Design Ragothaman M.Yennamalli, inEncyclopedia of Bioinformatics and Computational Biology, 2019 Conclusions Protein designis an active, exciting area of research that has wide applications in drug design, medicine, and advancing the study ofprotein folding. When designing protein structures, on...