We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction algorithms (cc\_analysis and encodermap) with a density-based spatial clustering algorithm (HDBSCAN). The proposed scheme benefits from the strengths of the three algorithms while avoiding most of the drawbacks of the individual methods. Here the cc\_analysis algorithm is for the first time applied to molecular simulation data. Encodermap complements cc\_analysis by providing an efficient way to process and assign large amounts of data to clusters. The main goal of the procedure is to maximize the number of assigned frames of a given trajectory, while keeping a clear conformational identity of the clusters that are found. In practice we achieve this by using an iterative clustering approach and a tunable root-mean-square-deviation-based criterion in the final cluster assignment. This allows to find clusters of different densities as well as different degrees of structural identity. With the help of four test systems we illustrate the capability and performance of this clustering workflow: wild-type and thermostable mutant of the Trp-cage protein (TC5b and TC10b), NTL9 and Protein B. Each of these systems poses individual challenges to the scheme, which in total give a nice overview of the advantages, as well as potential difficulties that can arise when using the proposed method.
A central partition of molecular conformational space. II. Embedding 3D structures
先前开发的分子构象空间的组合模型（J. Gabarro-Arpa，Comp. Biol. and Chem.27，（2003）153-159）具有这样的缺点，即结构不能被适当地嵌入，因为它缺乏明确的旋转对称性。这个问题可以通过将分子系统的基本3D组件分类到可以单独嵌入的有限类集合中来规避。这也开启了将动态状态编码到图结构中的可能性。
Hamming distance geometry of a protein conformational space. Application to the clustering of a 4 ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
Resonant Coupling Between Electromagnetic Waves and Protein Conformational Dynamics Revealed by Molecular Dynamics Simulations
The College of Medical Technology, Shanghai University of Medicine & Health Sciences（上海健康医学院医学技术学院）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）
Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation
Energy-Guided Generative Modeling for Low-Energy Molecular Structure Discovery
School of Artificial Intelligence, Shanghai Jiao Tong University（上海交通大学人工智能学院）；Department of Computer Science, National University of Singapore（新加坡国立大学计算机科学系）；Shenzhen International Graduate School, Tsinghua University（清华大学深圳国际研究生院）
Breaking the Timescale Barrier: Generative Discovery of Conformational Free-Energy Landscapes and Transition Pathways
Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦ 7019, Université de Lorraine（法国洛林大学）；Universidad Politécnica de Madrid（马德里理工大学）；University of Chicago（芝加哥大学）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Vib2Conf: AI-driven discrimination of molecular conformations from vibrational spectra
College of Chemistry and Chemical Engineering, Xiamen University（厦门大学化学化工学院）；Institute of Artificial Intelligence, Xiamen University（厦门大学人工智能研究院）；Shanghai Innovation Institute（上海创新研究院）；College of the Environment and Ecology, Xiamen University（厦门大学环境与生态学院）
Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment
Coarse-grained conformational surface hopping: Methodology and transferability
粗粒（CG）构象表面跳跃（SH）适应多表面动力学的概念，最初发展到描述化学反应中的电子跃迁，以准确地描述经典的分子动力学在一个减少的水平。SH方案耦合不同的构象盆地（状态），每个由其自身的力场（表面）描述，导致平均力的多体势近似的显著改进[Phys. Rev. Lett. 121，256002（2018）]。本研究首先介绍了CG SH更详细，通过一个玩具模型和三珠模型的己烷。我们进一步扩展的方法，以非键的相互作用，并报告其对液体性质的影响。最后，我们调查的可转移性的表面不同的系统和热力学状态点，通过一个简单的调整状态概率。特别是，应用程序的温度和化学成分的变化显示出良好的协议与参考原子计算，引入了一个有前途的“弱transferability制度”，其中CG力场可以共享热力学和化学邻域。
Reactive atomistic simulations of Diels-Alder-type reactions: Conformational and dynamic effects in the polar cycloaddition of 2,3-dibromobutadiene radical ions with maleic anhydride
用多表面绝热反应分子动力学方法对顺丁烯二酸酐与2，3-二溴丁二烯自由基离子的离子Diels-Alder反应（极性环加成）的动力学、动力学和构象特异性进行了理论研究.发现了协同和分步反应途径的竞争，并且二烯的s-顺式和s-反式构象都是反应性的。对反应最小动力学路径的分析表明，反应物分子的转动和振动对驱动体系向过渡态的转变都是重要的。在300 K的内部温度下，速率计算为2，3-二溴丁二烯的s-顺式构象的$k = 5.1 \times 10^{-14}$ s $^{-1}$和s-反式构象的$k = 3.8 \times 10^{-14}$ s $^{-1}$。目前的结果是要与标题系统的中性变体，其中只有二烯的笨拙构象被发现进行一个相当慢的，一致的，大多是同步的反应驱动的激励旋转。这里提出的结果通知详细的实验研究极性环加成反应的动力学在气相中的单碰撞条件下。
Hamiltonian replica exchange augmented with diffusion-based generative models and importance sampling to assess biomolecular conformational basins and barriers
