BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
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DOI：
10.1371/journal.pcbi.1008247
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发表时间：
2020-10
影响因子：
4.3
通讯作者：
Rose AS
中科院分区：
文献类型：
--
作者：
Sehnal D;Bittrich S;Velankar S;Koča J;Svobodová R;Burley SK;Rose AS
随着实验和计算结构确定方法的实质性进展，包括大分子结晶学、冷冻电子显微镜和综合方法，三维大分子结构数据变得越来越复杂和丰富。使用3D大分子结构数据进行存档、分析和可视化的有效手段是遵循公平原则促进互操作性和可重用性的核心。我们解决了数据大小和复杂性增长带来的两个挑战。首先，通过定制的压缩技术来减小数据大小。其次，通过改进软件工具和充分利用可用的数据字典模式来管理复杂性。为此，我们引入了BinaryCIF，这是晶体信息文件(CIF)格式文件的序列化，它保持了与相关数据模式(如PDBx/MmCIF)的完全兼容性，同时将文件大小减少了两倍以上，而不是gzip压缩的CIF文件。此外，对于最大的结构，BinaryCIF提供了比CIF文件和gzift CIF文件更好的压缩倍数10和4。在这里，我们描述CIFTools，这是一组Java和TypeScrip库，用于泛型和类型化处理CIF和BinaryCIF文件。BinaryCIF和CIFTools共同实现了对3D大分子结构数据的轻量级、高效和可扩展处理。
3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.
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影响因子：
64.8
作者：
Kim SJ;Fernandez-Martinez J;Nudelman I;Shi Y;Zhang W;Raveh B;Herricks T;Slaughter BD;Hogan JA;Upla P;Chemmama IE;Pellarin R;Echeverria I;Shivaraju M;Chaudhury AS;Wang J;Williams R;Unruh JR;Greenberg CH;Jacobs EY;Yu Z;de la Cruz MJ;Mironska R;Stokes DL;Aitchison JD;Jarrold MF;Gerton JL;Ludtke SJ;Akey CW;Chait BT;Sali A;Rout MP
通讯作者：
Rout MP
影响因子：
14.9
作者：
wwPDB consortium
通讯作者：
wwPDB consortium
影响因子：
5.8
作者：
Westbrook, J;Ito, N;Berman, HM
通讯作者：
Berman, HM
DOI：
10.1016/j.str.2018.03.011
发表时间：
2018-06-05
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Vallat B;Webb B;Westbrook JD;Sali A;Berman HM
通讯作者：
Berman HM
DOI：
10.1002/pro.3273
发表时间：
2018-01
期刊：
Protein science : a publication of the Protein Society
影响因子：
--
作者：
Kinjo AR;Bekker GJ;Wako H;Endo S;Tsuchiya Y;Sato H;Nishi H;Kinoshita K;Suzuki H;Kawabata T;Yokochi M;Iwata T;Kobayashi N;Fujiwara T;Kurisu G;Nakamura H
通讯作者：
Nakamura H