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狮子、老虎和熊,哦,我的天!计算机辅助分子设计的三大障碍。

Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design.

机构信息

Simulations Plus, Inc., Lancaster, CA 93534, USA.

出版信息

J Comput Aided Mol Des. 2012 Jan;26(1):29-34. doi: 10.1007/s10822-011-9504-3. Epub 2011 Dec 10.

DOI:10.1007/s10822-011-9504-3
PMID:22160503
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3268986/
Abstract

The computational chemistry and cheminformatics community faces many challenges to advancing the state of the art. We discuss three of those challenges here: accurately estimating the contribution of entropy to ligand binding; reliably estimating the uncertainties in model predictions for new molecules; and being able to effectively curate the ever-expanding literature and commercial databases needed to build new models.

摘要

计算化学和化学信息学领域在推动技术发展方面面临着诸多挑战。我们在这里讨论其中三个挑战:准确估计熵对配体结合的贡献;可靠估计新分子模型预测的不确定性;以及能够有效地管理不断扩展的文献和商业数据库,以构建新模型。

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J Phys Chem B. 2011 Jun 2;115(21):6811-7. doi: 10.1021/jp108493g. Epub 2011 May 10.
2
Design of multitarget activity landscapes that capture hierarchical activity cliff distributions.设计多靶点活性景观以捕获分层活性悬崖分布。
J Chem Inf Model. 2011 Feb 28;51(2):258-66. doi: 10.1021/ci100477m. Epub 2011 Jan 28.
3
PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.
QSAR 模型报告的最佳实践:物理化学性质、生态毒性、环境 fate、人类健康和毒代动力学终点。
Environ Health Perspect. 2018 Dec;126(12):126001. doi: 10.1289/EHP3264.
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PubChem chemical structure standardization.PubChem化学结构标准化
J Cheminform. 2018 Aug 10;10(1):36. doi: 10.1186/s13321-018-0293-8.
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Quantitative estimation of pesticide-likeness for agrochemical discovery.用于农用化学品发现的农药相似性定量评估。
J Cheminform. 2014 Sep 12;6(1):42. doi: 10.1186/s13321-014-0042-6. eCollection 2014 Dec.
6
From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions.从数据点时间轴到精心整理的数据集合,从科学文章中挖掘实验数据和化学结构数据,以及问题和可能的解决方案。
J Comput Aided Mol Des. 2013 Jul;27(7):583-603. doi: 10.1007/s10822-013-9664-4. Epub 2013 Jul 25.
7
Variability in docking success rates due to dataset preparation.由于数据集准备导致的对接成功率的变化。
J Comput Aided Mol Des. 2012 Jun;26(6):775-86. doi: 10.1007/s10822-012-9570-1. Epub 2012 May 8.
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