eMap 2.0: A Web-Based Platform for Identifying electron Transfer Pathways in Proteins and Protein Families [0.03%]
eMap 2.0：一个在蛋白质和蛋白质族中识别电子转移途径的网络平台
James R Gayvert,Alyssa J Kranc,Ruslan N Tazhigulov et al.
James R Gayvert et al.
In this review we present eMap 2.0, a web-based application for predicting electron/hole transfer pathways in proteins and protein families based on their structures. The underlying model can be viewed as a coarse-grained version of the Pat...
Path Integral-Free Energy Perturbation (PI-FEP) Simulations: Kinetic Isotope Effects of Proton/Deuteron Transfer Reactions in Aqueous Solution [0.03%]
不含路径积分的自由能PERTURBATION (PI-FEP)模拟：水溶液中质子/氘转移反应的动能同位素效应
Jiali Gao,Gavin Shuai Huang,Amber Simon et al.
Jiali Gao et al.
We present a tutorial review of the theoretical background and a step-by-step computational procedure for determining kinetic isotope effects (KIE) of chemical reactions in aqueous solution. The method combines path integral and free energy...
Jian Jiang,Lu Ke,Long Chen et al.
Jian Jiang et al.
A transformer is the foundational architecture behind large language models designed to handle sequential data by using mechanisms of self-attention to weigh the importance of different elements, enabling efficient processing and understand...
Fragme∩t: An Open-Source Framework for Multiscale Quantum Chemistry Based on Fragmentation [0.03%]
基于片段法的多尺度量子化学开源框架Fragme∩t
Dustin R Broderick,Paige E Bowling,Chance Brandt et al.
Dustin R Broderick et al.
Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations by partitioning a large calculation into smaller subsystems, then considering the many-body ...
Weighted Ensemble Simulation: Advances in methods, software, and applications [0.03%]
加权集合模拟方法、软件和应用的新进展
Lillian T Chong,Daniel M Zuckerman
Lillian T Chong
For more than two decades, weighted ensemble (WE) path sampling strategies have enabled the simulation of pathways for rare events-or barrier-crossing processes-with significantly less computing cost than conventional simulations, all while...
Yangyi Lu,Jiali Gao
Yangyi Lu
A quantum theory of density functionals and its applications is presented. By introducing a matrix density D ( r ) of rank N as the fundamental variable, a one-to-one correspondence has been established between D ( r ) and the Hamiltonian m...
Revolutionizing Peptide-Based Drug Discovery: Advances in the Post-AlphaFold Era [0.03%]
后AlphaFold时代肽类药物发现的进展：革命与展望
Liwei Chang,Arup Mondal,Bhumika Singh et al.
Liwei Chang et al.
Peptide-based drugs offer high specificity, potency, and selectivity. However, their inherent flexibility and differences in conformational preferences between their free and bound states create unique challenges that have hindered progress...
Yuanzhe Zhou,Yangwei Jiang,Shi-Jie Chen
Yuanzhe Zhou
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions...
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case [0.03%]
用于分子动力学模拟的预exascale HPC方法：Covid-19研究用例
Miłosz Wieczór,Vito Genna,Juan Aranda et al.
Miłosz Wieczór et al.
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomo...
In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways [0.03%]
计算毒理学：从构效关系到深度学习和不良结局途径
Jennifer Hemmerich,Gerhard F Ecker
Jennifer Hemmerich
In silico toxicology is an emerging field. It gains increasing importance as research is aiming to decrease the use of animal experiments as suggested in the 3R principles by Russell and Burch. In silico toxicology is a means to identify ha...