干旱区生态环境知识资源中心(Arid): IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

Arid

DOI	10.1107/S1600576719015115
	IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination
	Ding, Wei 1; Zhang, Tao 1; He, Yao 1; Wang, Jiawei 2; Wu, Lijie 3; Pu, Han 1; Zheng, Chaode 1; Gu, Yuanxin 1; Zeng, Lingxiao 4; Hao, Quan 4; Fan, Haifu 1
通讯作者	Ding, Wei ; Hao, Quan
来源期刊	JOURNAL OF APPLIED CRYSTALLOGRAPHY
ISSN	0021-8898
EISSN	1600-5767
出版年	2020
卷号	53 页码:253-261
英文摘要	A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including 'direct-method phasing and fragment extension' from weak anomalous diffraction signal data and 'direct-method-aided partial-structure extension' from low-homology models.
英文关键词	OASIS IPCAS direct methods protein crystallography single-particle cryo-EM image processing
类型	Article
语种	英语
国家	Peoples R China
收录类别	SCI-E
WOS记录号	WOS:000512316900029
WOS关键词	MOLECULAR-REPLACEMENT ; CRYSTAL-STRUCTURE ; ISOMORPHOUS REPLACEMENT ; DENSITY MODIFICATION ; CCP4 SUITE ; MAPS
WOS类目	Chemistry, Multidisciplinary ; Crystallography
WOS研究方向	Chemistry ; Crystallography
来源机构	清华大学
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/314862
作者单位	1.Chinese Acad Sci, Inst Phys, CAS Key Lab Soft Matter Phys, POB 603, Beijing 100190, Peoples R China; 2.Tsinghua Univ, Sch Life Sci, Beijing 100084, Peoples R China; 3.Chinese Acad Sci, Natl Ctr Prot Sci Shanghai, Inst Biochem & Cell Biol, Shanghai Inst Biol Sci,State Key Lab Mol Biol, Shanghai 200031, Peoples R China; 4.Univ Hong Kong, Sch Biomed Sci, Hong Kong, Peoples R China
推荐引用方式 GB/T 7714	Ding, Wei,Zhang, Tao,He, Yao,et al. IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination[J]. 清华大学,2020,53:253-261.
APA	Ding, Wei.,Zhang, Tao.,He, Yao.,Wang, Jiawei.,Wu, Lijie.,...&Fan, Haifu.(2020).IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination.JOURNAL OF APPLIED CRYSTALLOGRAPHY,53,253-261.
MLA	Ding, Wei,et al."IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination".JOURNAL OF APPLIED CRYSTALLOGRAPHY 53(2020):253-261.