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...
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
a, Like all repeating structures, repeat proteins and peptides form superhelices with constant axial displacement (ΔZ) and angular twist (ω) between adjacent repeat units (shown in green and yellow). For in-register binding, the protein and peptide parameters must match (for some integral mul...
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...
interactionsinvolvedinbinding.Herewedescribeageneralcom- putationalmethodfordesigningpre-organizedandshapecomple- mentarysmall-molecule-bindingsites,anduseittogenerateprotein binderstothesteroiddigoxigenin(DIG).Ofseventeenexperimentally characterizeddesigns,twobindDIG;themodelofthehigheraffinity ...
Designing proteins that bind to a given ligand has long been a dream of many chemists. With the accumulated structural information on protein–ligand complexes, experimental data on thermodynamics and kinetics of binding [9], and developments in related theories [10, 11], much has been learned ...
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 ...
Validation demonstrates a high level of accuracy for the algorithm.http://www.ehscenter.org/dbd/ Supplementary information: http://www.ehscenter.org/dbd/ 展开 关键词: Algorithms Computer-Aided Design Disulfides Drug Design Protein Binding 算法 计算机辅助设计 二硫化物类 药物设计 蛋白质结合 ...
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 ...