• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

柔性底座:一种增强分子对接方法应用的途径。

Flexibases: a way to enhance the use of molecular docking methods.

作者信息

Kearsley S K, Underwood D J, Sheridan R P, Miller M D

机构信息

Department of Molecular Systems, Merck Research Laboratories, Rahway, NJ 07065.

出版信息

J Comput Aided Mol Des. 1994 Oct;8(5):565-82. doi: 10.1007/BF00123666.

DOI:10.1007/BF00123666
PMID:7876901
Abstract

Specially expanded databases containing three-dimensional structures are created to enhance the utility of docking methods to find new leads, i.e., active compounds of pharmacological interest. The expansion is based on the automatic generation of a set of maximally dissimilar conformations. The ligand receptor system of methotrexate and dihydrofolate reductase is used to demonstrate the feasibility of creating flexibases and their utility in docking studies.

摘要

创建了包含三维结构的特殊扩展数据库,以提高对接方法寻找新先导物(即具有药理学意义的活性化合物)的效用。这种扩展基于自动生成一组最大程度不同的构象。使用甲氨蝶呤和二氢叶酸还原酶的配体受体系统来证明创建柔性库的可行性及其在对接研究中的效用。

相似文献

1
Flexibases: a way to enhance the use of molecular docking methods.柔性底座:一种增强分子对接方法应用的途径。
J Comput Aided Mol Des. 1994 Oct;8(5):565-82. doi: 10.1007/BF00123666.
2
FlexE: efficient molecular docking considering protein structure variations.FlexE:考虑蛋白质结构变异的高效分子对接
J Mol Biol. 2001 Apr 27;308(2):377-95. doi: 10.1006/jmbi.2001.4551.
3
Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.通过配体 - 蛋白质相互作用的计算机模拟来理解分子识别机制。
J Mol Recognit. 1999 Nov-Dec;12(6):371-89. doi: 10.1002/(SICI)1099-1352(199911/12)12:6<371::AID-JMR479>3.0.CO;2-O.
4
Towards a MIP-based alignment and docking in computer-aided drug design.迈向计算机辅助药物设计中基于MIP的比对和对接
Proteins. 2004 Aug 15;56(3):585-94. doi: 10.1002/prot.20153.
5
FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure.FLOG:一种用于选择与已知三维结构受体互补的“准柔性”配体的系统。
J Comput Aided Mol Des. 1994 Apr;8(2):153-74. doi: 10.1007/BF00119865.
6
Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation.
J Med Chem. 1993 Oct 1;36(20):2921-8. doi: 10.1021/jm00072a011.
7
A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors.一种提高比较分子场分析(CoMFA)模型预测能力的新方法及其在一组二氢叶酸还原酶抑制剂中的应用。
J Comput Aided Mol Des. 1995 Oct;9(5):396-406. doi: 10.1007/BF00123997.
8
Rational automatic search method for stable docking models of protein and ligand.蛋白质与配体稳定对接模型的合理自动搜索方法
J Mol Biol. 1994 Oct 21;243(2):310-26. doi: 10.1006/jmbi.1994.1656.
9
Pharmacophore-based molecular docking to account for ligand flexibility.基于药效团的分子对接以考虑配体柔性。
Proteins. 2003 May 1;51(2):172-88. doi: 10.1002/prot.10266.
10
Design of libraries to explore receptor sites.用于探索受体位点的文库设计。
J Chem Inf Comput Sci. 1999 Jan-Feb;39(1):46-50. doi: 10.1021/ci980104h.

引用本文的文献

1
RNA-ligand molecular docking: advances and challenges.RNA-配体分子对接:进展与挑战
Wiley Interdiscip Rev Comput Mol Sci. 2022 May-Jun;12(3). doi: 10.1002/wcms.1571. Epub 2021 Aug 16.
2
Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening.高通量虚拟筛选共识对接综合调查。
Molecules. 2022 Dec 25;28(1):175. doi: 10.3390/molecules28010175.
3
Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening.基于大规模结构的虚拟筛选中对接失败的系统研究。

本文引用的文献

1
FOUNDATION: a program to retrieve all possible structures containing a user-defined minimum number of matching query elements from three-dimensional databases.
J Comput Aided Mol Des. 1993 Feb;7(1):3-22. doi: 10.1007/BF00141572.
2
GenStar: a method for de novo drug design.GenStar:一种全新药物设计方法。
J Comput Aided Mol Des. 1993 Feb;7(1):23-43. doi: 10.1007/BF00141573.
3
An exploration of a novel strategy for superposing several flexible molecules.一种叠加多个柔性分子的新策略的探索。
ACS Omega. 2022 Oct 17;7(43):39417-39428. doi: 10.1021/acsomega.2c05826. eCollection 2022 Nov 1.
4
Protein-Ligand Docking in the Machine-Learning Era.蛋白质-配体对接在机器学习时代。
Molecules. 2022 Jul 18;27(14):4568. doi: 10.3390/molecules27144568.
5
Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets.章鱼:一个针对一组分子靶点对化合物库进行虚拟高通量筛选的平台。
J Mol Model. 2017 Jan;23(1):26. doi: 10.1007/s00894-016-3184-9. Epub 2017 Jan 7.
6
Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods.蛋白质-配体相互作用的见解:机制、模型与方法
Int J Mol Sci. 2016 Jan 26;17(2):144. doi: 10.3390/ijms17020144.
7
Ligand pose and orientational sampling in molecular docking.分子对接中的配体构象与取向采样
PLoS One. 2013 Oct 1;8(10):e75992. doi: 10.1371/journal.pone.0075992. eCollection 2013.
8
Drug design for ever, from hype to hope.药物设计永不止步,从炒作到希望。
J Comput Aided Mol Des. 2012 Jan;26(1):137-50. doi: 10.1007/s10822-011-9519-9. Epub 2012 Jan 18.
9
Docking validation resources: protein family and ligand flexibility experiments.对接验证资源:蛋白质家族和配体柔性实验。
J Chem Inf Model. 2010 Nov 22;50(11):1986-2000. doi: 10.1021/ci1001982. Epub 2010 Oct 29.
10
Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database.使用 OMEGA 生成构象:使用来自蛋白质数据库和剑桥结构数据库的高质量结构进行算法验证。
J Chem Inf Model. 2010 Apr 26;50(4):572-84. doi: 10.1021/ci100031x.
J Comput Aided Mol Des. 1993 Apr;7(2):155-72. doi: 10.1007/BF00126442.
4
SPROUT: a program for structure generation.
J Comput Aided Mol Des. 1993 Apr;7(2):127-53. doi: 10.1007/BF00126441.
5
FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure.FLOG:一种用于选择与已知三维结构受体互补的“准柔性”配体的系统。
J Comput Aided Mol Des. 1994 Apr;8(2):153-74. doi: 10.1007/BF00119865.
6
A geometric approach to macromolecule-ligand interactions.一种研究大分子-配体相互作用的几何方法。
J Mol Biol. 1982 Oct 25;161(2):269-88. doi: 10.1016/0022-2836(82)90153-x.
7
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.大肠杆菌和干酪乳杆菌二氢叶酸还原酶在1.7埃分辨率下的晶体结构。II. 结合的NADPH的环境及其对催化作用的影响。
J Biol Chem. 1982 Nov 25;257(22):13663-72.
8
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.大肠杆菌和干酪乳杆菌二氢叶酸还原酶的晶体结构在1.7埃分辨率下的精修。I. 甲氨蝶呤的一般特征和结合情况
J Biol Chem. 1982 Nov 25;257(22):13650-62.
9
Docking flexible ligands to macromolecular receptors by molecular shape.通过分子形状将柔性配体对接至大分子受体
J Med Chem. 1986 Nov;29(11):2149-53. doi: 10.1021/jm00161a004.
10
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.利用形状互补性作为初步筛选方法,来设计针对已知三维结构受体结合位点的配体。
J Med Chem. 1988 Apr;31(4):722-9. doi: 10.1021/jm00399a006.