Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA, 15213, USA.
Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan.
Nucleic Acids Res. 2017 Jul 3;45(W1):W374-W380. doi: 10.1093/nar/gkx385.
DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)-the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein-protein and protein-DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The 'environment' is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http://enm.pitt.edu/ or http://dyn.life.nthu.edu.tw/oENM/.
DynOmics（dynomics.pitt.edu）是一个门户，旨在通过有效地、准确地评估在生理环境中结构解析系统（从单个分子到大型复合物和组装体）的动力学，利用快速增长的结构蛋白质组学数据。该门户的核心是一个新开发的服务器 ENM 1.0，它允许用户有效地生成任何 PDB 格式结构的集体动力学信息，无论是用户上传的还是从数据库检索的。ENM 1.0 集成了两种广泛使用的弹性网络模型（ENMs）——高斯网络模型（GNM）和各向异性网络模型（ANM），并扩展到考虑分子环境。它使用户能够评估潜在的功能位点、信号转导或变构通讯机制，以及蛋白质-蛋白质和蛋白质-DNA 相互作用构象，此外还可以根据由 ANM 预测的全局运动模式，以原子细节重建可及构象的集合。“环境”以灵活的方式定义，从脂质双层和晶体接触，到与蛋白质结合的底物或配体，或多聚体结构或组装体周围的亚基。用户友好的交互功能允许用户轻松地可视化环境如何改变查询系统的固有动力学。ENM 1.0 可在 http://enm.pitt.edu/ 或 http://dyn.life.nthu.edu.tw/oENM/ 访问。
