The PCDDB project: Tools and resources for CD analyses, archiving, display, and sharing
The PCDDB project: Tools and resources for CD analyses, archiving, display, and sharing
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PCDDB 项目：用于 CD 分析、存档、显示和共享的工具和资源
DOI：
10.1016/j.bpj.2022.11.1080
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发表时间：
2023
影响因子：
3.4
通讯作者：
Wallace B
中科院分区：
文献类型：
--
作者：
Wallace B
蛋白质圆二色性数据库项目于20多年前启动，旨在创建一套集成的软件和工具，以帮助圆二色性（CD）和同步辐射圆二色性（SRCD）光谱和元数据的分析，解释，视觉显示和数据共享。它是创造各种新颖的生物物理和计算方法的基础，是我们两个实验室和许多合作者协调努力的结果。其核心是DichroWeb分析服务器，该服务器已被超过9000名用户用于200万次二级结构分析，其中包括创建新的计算方法和相关的参考数据库，用于检查可溶性，膜和内在无序蛋白质。PCDDB本身是作为CD数据和元数据的储存库创建的，与广泛的生物信息学，计算和结构数据库和工具相链接，鼓励CD和其他生物物理方法的互操作性。它包括链接到一级序列（UniProt）和结构（PDB）数据库，以及二级数据库，如酶委员会功能数据库和CATH折叠数据库。此外，还创建了用于数据处理和显示CD光谱的工具，用于验证光谱质量（ValiDichro），用于与其他方法（如PDB2CD，PDBMD2CD，2StructCompare）集成。和DichroCompare，加上新的可视化方法，包括蛋白质折叠动力学。创建的软件可通过GitHub在线获得。除了提供广泛使用的研究工具外，该项目也是世界各地CD暑期学校和课程的核心教学工具，并受益于世界各地许多生物制药团体的贡献。[由BBSRC的英国生物技术和生物资源计划赠款]。
The Protein Circular Dichroism Data Bank Project was initiated more than 20 years ago as a means of creating an integrated set of software and tools to aid in analyses, interpretations, visual displays, and data sharing of circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and metadata. It has been a basis for the creation of a wide range of novel biophysical and computational methods, and has resulted from the coordinated effort of our two labs and many collaborators. At its heart has been the DichroWeb analysis server, which has been used for∼ 2 M secondary structure analyses by> 9000 users, and which has included the creation of new computational methods and associated reference databases for examining soluble, membrane, and intrinsically-disordered proteins. The PCDDB itself was created as a repository for CD data and metadata with links to a wide range of bioinformatics, computational, and structural databases and tools, encouraging interoperability of CD and other biophysical methods. It includes links to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional database and the CATH fold database. In addition, tools were created for data processing, and display of CD spectra, for validation of spectral quality (ValiDichro), for integration with other methods such as PDB2CD, PDBMD2CD, 2StructCompare. and DichroCompare, plus novel methods of visualisation, including kinetics of protein folding. Software created is available online via GitHub. In addition to providing widely-used research tools, this project has also been the core teaching tool for CD summer schools and courses worldwide, and has benefitted from the contributions of many biophysicis groups worldwide.[Supported by grants from the UK Biotechnology and Biological Resources programme of the BBSRC).