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Simulating the ion permeation and ion selection for a eukaryotic voltage-gated sodium channel NaVPaS

the Ministry of Science and Technology of China (No. 2015CB910100) as well as the Beijing Advanced Innovation Center for Structural Biology. Juanrong Zhang, Wenzhi Mao, Yanhui Ren, Rui-Ning Sun, Nieng ... indicate if changes were made. Juanrong Zhang, Wenzhi Mao, and Yanhui Ren contributed equally to the work. Electronic supplementary material The online version of this article (https://doi.org/10.1007

Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution

Motivation: With rapid accumulation of sequence data on several species, extracting rational and systematic information from multiple sequence alignments (MSAs) is becoming increasingly important. Currently, there is a plethora of computational methods for investigating coupled evolutionary changes in pairs of positions along the amino acid sequence, and making inferences on...

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from...

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70...