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...
Mechanisms, Challenges, and Opportunities of Dual Ni/Photoredox-Catalyzed C(sp2)-C(sp3) Cross-Couplings [0.03%]
双Ni/光氧化还原催化C(sp2)-C(sp3)交叉偶联的机制、挑战和机遇
Mingbin Yuan,Osvaldo Gutierrez
Mingbin Yuan
The merging of photoredox and nickel catalysis has revolutionized the field of C-C cross-coupling. However, in comparison to the development of synthetic methods, detailed mechanistic investigations of these catalytic systems are lagging. T...
From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic [0.03%]
从量子衍生的半胱氨酸反应性原理到抗击COVID-19疫情
Karine Mazmanian,Ting Chen,Karen Sargsyan et al.
Karine Mazmanian et al.
The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/c...
Gaussian accelerated molecular dynamics (GaMD): principles and applications [0.03%]
高斯加速分子动力学(GaMD)：原理与应用
Jinan Wang,Pablo R Arantes,Apurba Bhattarai et al.
Jinan Wang et al.
Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecu...
Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials [0.03%]
具有先进极化势的量子力学/分子力学方法的发展与应用
Jorge Nochebuena,Sehr Naseem-Khan,G Andrés Cisneros
Jorge Nochebuena
Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and bi...