Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require. Currently there is no available method of protein 3D structure representation which captures enough chemical information from the protein sequence and clearly shows the intra-molecular and the inter-molecular H-bonds and VDW interactions at the same time. This project aims to reduce the 3D structure of a protein and display the reduced representation along with intermolecular and the intra- molecular H-bonds and van der Waals interactions. A reduced protein representation has a significantly lower atomicity (i.e., number of atom coordinates) than one which is in all- atom representation. In this work, we transform the protein structure from all-atom representation" (AAR) to double-centroid reduced representation (DCRR), which contains amino acid backbone (N, CA, C', O) and side chain (CB and beyond) centroid coordinates instead of atomic coordinates. Another aim of this project is to develop a visualization interface for the reduced representation. This interface is implemented in MATLAB and displays the protein in DCRR along with its inter-molecular, as well as intra-molecular, interaction. Visually, DCRR is easier to comprehend than AAR. We also developed a Web Server called the Protein DCRR Web Server wherein users can enter the PDB id or upload a modeled protein and get the DCRR of that protein. The back end to the Web Server is a database which has the reduced representation for all the x-ray crystallographic structure in the PDB.
The eBDIMS path-sampling server: generation, classification and interactive visualization of protein ensembles and transition pathways in 2D-motion space
Intuitive representation of surface properties of biomolecules using BioBlender
在Zini等人的这篇和相关文章“BioBlender：Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine”中，我们提出了BioBlender，一个完整的工具，用于阐述运动（Zini等人）。以及蛋白质和其他大分子的可视化（这里），使用计算机图形工具。蛋白质结构的可用性使得能够基于原子贡献来研究它们的表面和表面性质，例如静电势（EP）和亲水性（MLP）。3D动画和渲染软件的最新进展尚未用于以直观的动画形式表示蛋白质和其他生物分子。利用开源的3D动画和渲染软件Blender，我们开发了BioBlender，这是一个专门用于生物工作的软件包：详细说明蛋白质的运动，同时可视化化学和物理特征。EP和MLP使用物理化学程序和自定义程序和脚本计算，在BioBlender界面中组织和访问。一个新的视觉代码引入MLP可视化：一系列的光学功能，允许其在蛋白质表面上的空间分布的逼真渲染。EP被表示为沿着与蛋白质的总电荷成比例的场线流动的动画线粒子。我们的系统允许EP和MLP可视化的分子，并在移动的蛋白质的情况下，这些功能的连续感知，计算每个中间构象。使用真实世界的触觉/视觉感觉，蛋白质的纳米级世界变得更容易理解，更熟悉我们的日常生活，更容易引入“看不见”的现象（概念），如亲水性或电荷。
Entropy Transfer Throughout the Structure of PDZ-2 and TIM-Barrel Proteins. A Dynamic Gaussian Network Model Study
Facultad de Ingenieria Ciencia y Tecnologia, Universidad Bernardo O'Higgins（贝尔纳多·奥希金斯大学）；Departamento de Ciencias Fisicas, Facultad de Ciencias Exactas, Universidad Andres Bello（安德烈斯·贝略大学）；Departamento de Mathematica y Ciencias de la Computacion, Universidad de Santiago de Chile（智利圣地亚哥大学）
Molecular architecture of TE-seeded chromosome-naive initiation networks of protein-protein interactions delineates the Human Protein Map of the assembly of multiprotein complexes
Institute of Engineering in Medicine University of California, San Diego（加州大学圣地亚哥分校工程医学院）
