Department of Physics, University of Cyprus, Nicosia, Cyprus.
STAR Protoc. 2022 Mar 3;3(2):101254. doi: 10.1016/j.xpro.2022.101254. eCollection 2022 Jun 17.
The present protocol describes the computational design of the SARS-CoV-2 receptor binding motif (RBD) to identify mutations that can potentially improve binding affinity for the human ACE2 (hACE2) receptor. We focus on four positions located at the interface with the hACE2 receptor in the RBD:hACE2 complex. We conduct the design with a high-throughput computational protein design (CPD) program, Proteus, incorporating an adaptive Monte Carlo (MC) protocol that promotes the selection of sequences with good binding affinities. For complete details on the use and execution of this protocol, please refer to Polydorides and Archontis (2021).
本方案描述了 SARS-CoV-2 受体结合基序（RBD）的计算设计，以鉴定可能提高与人类 ACE2（hACE2）受体结合亲和力的突变。我们专注于 RBD:hACE2 复合物中与 hACE2 受体相互作用的四个位置。我们使用高通量计算蛋白质设计（CPD）程序 Proteus 进行设计，该程序包含一个自适应蒙特卡罗（MC）协议，可促进选择具有良好结合亲和力的序列。有关使用和执行本方案的完整详细信息，请参见 Polydorides 和 Archontis（2021）。
