Software Maintenance for Biomolecular Complexes

生物分子复合物的软件维护

• 批准号: 7569330
• 负责人: CHANDRAJIT L BAJAJ
• 金额: $ 29.24万
• 依托单位: UNIVERSITY OF TEXAS AT AUSTIN
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-02-15 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7569330
• 关键词: Algorithms; Binding; Biochemistry; Bioinformatics; Biological Process; Biophysics; Charge; Communities; Complex; Computational Biology; Computer software; Cryoelectron Microscopy; Data; Databases; Deposition; Development; Disease; Documentation; Electrons; Electrostatics; Elements; Environment; European; Feedback; Generations; Hybrids; Image; Imagery; Individual; Institutes; Internet; Knowledge; Letters; Libraries; Licensing; Maintenance; Malignant Neoplasms; Maps; Metabolic Diseases; Modeling; Molecular; Molecular Models; NMR Spectroscopy; Online Systems; Output; Process; Property; Proteins; Proteomics; Public Domains; Research; Research Personnel; Sampling; Software Tools; Structure; Surface; Techniques; Testing; Texture; Therapeutic Intervention; Visual; Visualization software; X-Ray Crystallography; base; density; flexibility; image processing; interest; macromolecule; molecular modeling; open source; programs; response; simulation; supercomputer; three dimensional structure; three-dimensional modeling; tool

DESCRIPTION (provided by applicant): We have developed an integrated Molecular Visualization and Processing environment (MVP) consisting of volumetric image processing, finite element meshing, analysis and rendering libraries (Filter, Classify, Segment, TetMesh, HexMesh, Analyze, Contour, VolRend, and TexRend) and software tools: an interactive Volumetric map exploration and processing tool (Vol Rover) primarily for 3D maps, an interactive syntheticTexture Molecular visualization and processing tool (TexMol) primarily for large structure models, and a Level Set Bounded Interior Exterior boundary/finite element Meshing tool (LBIE-Mesher) for macromolecules, and for aiding boundary and finite element based computation of associated properties. Based on user feedback, and our research agenda in volumetric image processing, computational geometry and Visualization, we propose a three-pronged continued development, maintenance and distribution plan of our software base. More precisely, our specific aims are: 1. Continued development of algorithms and data structures which support our MVP and provide enhanced volumetric and geometry processing, meshing, analysis and rendering. These algorithms include new developments in fast and automatic identification of folds and structure units in 3D Maps, hierarchical data structures that support multiresolution molecular surfaces, quality and topologically accurate finite element meshing and automatic region of interest identification. 2. Continued maintenance development and testing of the software libraries and tools in our MVP to provide enhanced volumetric map and geometry processing, meshing, analysis and rendering techniques for larger macromolecules. This software includes accelerated techniques through a combined use of multiresolution, compression, and Programmable Graphics Processor (PGP) utilization. 3. Continued documentation and web based dissemination of all the components (libraries and tools) of our MVP. (http://ccvweb.csres.utexas.edu/software/).

描述（由申请人提供）：我们开发了一个集成的分子可视化和处理环境（MVP），由体积图像处理、有限元网格划分、分析和渲染库（Filter、Classify、Segment、TetMesh、HexMesh、Analyze、Contour、VolRend）组成和 TexRend）和软件工具：主要用于 3D 地图的交互式体积图探索和处理工具（Vol Rover）、交互式合成纹理分子可视化和处理工具(TexMol) 主要用于大型结构模型，水平集有界内部外部边界/有限元网格划分工具 (LBIE-Mesher) 用于大分子，并用于辅助基于边界和有限元的相关属性计算。根据用户反馈以及我们在体积图像处理、计算几何和可视化方面的研究议程，我们提出了软件库的三管齐下的持续开发、维护和分发计划。更准确地说，我们的具体目标是： 1. 持续开发算法和数据结构，支持我们的 MVP 并提供增强的体积和几何处理、网格划分、分析和渲染。这些算法包括快速自动识别 3D 地图中的折叠和结构单元、支持多分辨率分子表面的分层数据结构、质量和拓扑精确的有限元网格划分以及自动感兴趣区域识别方面的新发展。 2. 继续维护开发和测试 MVP 中的软件库和工具，为更大的大分子提供增强的体积图和几何处理、网格划分、分析和渲染技术。该软件包括通过结合使用多分辨率、压缩和可编程图形处理器 (PGP) 使用的加速技术。 3. 继续对 MVP 的所有组件（库和工具）进行文档化和基于网络的传播。 （http://ccvweb.csres.utexas.edu/software/）。