D3PM: a comprehensive database for protein motions ranging from residue to domain
文献类型：期刊论文
| 作者 | Peng,Cheng2,3; Zhang,Xinben3; Xu,Zhijian2,3 ; Chen,Zhaoqiang3; Yang,Yanqing2,3; Cai,Tingting3; Zhu,Weiliang1,2,3
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| 刊名 | BMC Bioinformatics
 |
| 出版日期 | 2022-02-14 |
| 卷号 | 23期号:1 |
| 关键词 | Protein motion Motion pattern D3PM database Amino acids preference |
| DOI | 10.1186/s12859-022-04595-0 |
| 通讯作者 | Xu,Zhijian(zjxu@simm.ac.cn) ; Zhu,Weiliang(wlzhu@simm.ac.cn) |
| 英文摘要 | AbstractBackgroundKnowledge of protein motions is significant to understand its functions. While currently available databases for protein motions are mostly focused on overall domain motions, little attention is paid on local residue motions. Albeit with relatively small scale, the local residue motions, especially those residues in binding pockets, may play crucial roles in protein functioning and ligands binding.ResultsA comprehensive protein motion database, namely D3PM, was constructed in this study to facilitate the analysis of protein motions. The protein motions in the D3PM range from overall structural changes of macromolecule to local flip motions of binding pocket residues. Currently, the D3PM has collected 7679 proteins with overall motions and 3513 proteins with pocket residue motions. The motion patterns are classified into 4 types of overall structural changes and 5 types of pocket residue motions. Impressively, we found that less than 15% of protein pairs have obvious overall conformational adaptations induced by ligand binding, while more than 50% of protein pairs have significant structural changes in ligand binding sites, indicating that ligand-induced conformational changes are drastic and mainly confined around ligand binding sites. Based on the residue preference in binding pocket, we classified amino acids into “pocketphilic” and “pocketphobic” residues, which should be helpful for pocket prediction and drug design.ConclusionD3PM is a comprehensive database about protein motions ranging from residue to domain, which should be useful for exploring diverse protein motions and for understanding protein function and drug design. The D3PM is available on www.d3pharma.com/D3PM/index.php. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/S12859-022-04595-0 |
| 出版者 | BioMed Central |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/300127]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Xu,Zhijian; Zhu,Weiliang |
| 作者单位 | 1.Pilot National Laboratory for Marine Science and Technology (Qingdao); Open Studio for Druggability Research of Marine Natural Products 2.University of Chinese Academy of Sciences 3.Chinese Academy of Sciences; CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica |
| 推荐引用方式 GB/T 7714 | Peng,Cheng,Zhang,Xinben,Xu,Zhijian,et al. D3PM: a comprehensive database for protein motions ranging from residue to domain[J]. BMC Bioinformatics,2022,23(1). |
| APA | Peng,Cheng.,Zhang,Xinben.,Xu,Zhijian.,Chen,Zhaoqiang.,Yang,Yanqing.,...&Zhu,Weiliang.(2022).D3PM: a comprehensive database for protein motions ranging from residue to domain.BMC Bioinformatics,23(1). |
| MLA | Peng,Cheng,et al."D3PM: a comprehensive database for protein motions ranging from residue to domain".BMC Bioinformatics 23.1(2022). |
入库方式： OAI收割
来源：上海药物研究所
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