Taba: A Tool to Analyze the Binding Affinity

Evaluation of ligand-binding affinity using the atomic coordinates of a protein-ligand complex is a challenge from the computational point of view. The availability of crystallographic structures of complexes with binding affinity data opens the possibility to create machine-learning models targeted to a specific protein system. Here, we describe a new methodology that combines a mass-spring system approach with supervised machine-learning techniques to predict the binding affinity of protein-ligand complexes. The combination of these techniques allows exploring the scoring function space, generating a model targeted to a protein system of interest. The new model shows superior predictive performance when compared with classical scoring functions implemented in the programs Molegro Virtual Docker, AutoDock4, and AutoDock Vina. We implemented this methodology in a new program named Taba. Taba is implemented in Python and available to download under the GNU license at https://github.com/azevedolab/taba . © 2019 Wiley Periodicals, Inc.     

结合PBL的思维导图法在大学化学“四大平衡”教学中的应用

Taking the chemical equilibria including acid-base equilibrium, complexation equilibrium, precipitation equilibrium and redox equilibrium as an example, the application of the mind mapping combined with problem-based learning in university chemistry teaching is introduced.     

人工智能助力当代化学研究

以机器学习为代表的人工智能在当代的科学研究中正在发挥越来越重要的作用.不同于传统的计算机程序,机器学习人工智能可以通过对大量数据的反复分析和自身模型的优化,即“学习”过程,从而在大量的数据中寻找客观事物的相互联系,形成具有更好预测和决策能力的新模型,做出合理的判断.化学研究的特点恰恰是机器学习人工智能的强项.化学研究经常要面对十分复杂的物质体系和实验过程,从而很难通过化学物理原理进行精准的分析和判断.人工智能可以挖掘化学实验中产生的海量实验数据的相关性,帮助化学家做出合理分析预测,大大加速化学研发过程.本文介绍了当代人工智能方法及用其解决化学问题基本原理,并通过具体案例展示了人工智能辅助解决不同化学研发问题的方法以及对应的机器学习算法.将人工智能运用在化学科学的尝试正处于蓬勃上升期,人工智能已经初步展示出对化学研究的强大助力,希望本文能帮助更多的国内的化学工作者了解和运用这一有力的工具.     

利用有机波谱教学网站iSpec进行游戏化课堂教学的实践*

针对学生在有机化学波谱学学习过程中枯燥、难以形象化的具体情况,介绍一个利用有机波谱在线学习的网站进行游戏化课堂教学的学习活动,以期提升学生在该课程学习中的积极性及学习效果。该教学活动的实施分为课堂和课后进行,主要依托iSpec网站游戏竞赛的答题模式,结合教师课堂教学及学生自主学习,进行相关知识技能的教授,最终提升学生的学习效率与效果。     

案例教学与翻转学习结合提升物理化学教学质量

结合我校应用型人才培养方案和培养目标,通过改革物理化学课堂教学提高学生知识掌握能力和应用能力。在传统课堂的基础上,将案例教学结合在翻转学习的教学过程中,充分提高学生的学习积极性与主动性。以稀溶液的依数性为教学案例,阐述翻转学习与案例教学的实施过程。学生深度参与课堂、融入课堂并互动,师生之间在教学中达到共鸣,实现教学相长,从而提高物理化学教学质量。     

Cheminformatics in MS-based environmental exposomics: Current achievements and future directions

Compound annotation using MS/MS data is the major bottleneck in interpretation of mass spectrometry data during non-targeted screening and suspect screening exposomics studies. Apart from compound identification using available databases or mass spectral libraries, the true challenge comes when completely new compounds have to be identified. Along with recent advances in MS instrumentation that set grounds to a new revolutionary age in environmental exposomics, a multitude of cheminformatics annotation approaches has been developed. Herein, we review the basic principles of the cutting-edge cheminformatics MS-based approaches employed in eco-exposome annotation.We give a solid background discussing the eco-exposome concept in relation to the advances in MS instrumentation, and define the three crucial cheminformatics tasks used in the eco-exposome annotation: molecular formula assignment, compound prioritization and compound annotation. The basic principles of compound annotation are discussed, which are based on three approaches of utilizing structural information inherent to MS data. These involve direct, indirect and joint annotation approaches. We assess their performance through the ability to annotate eco-exposome constituents. We discuss future perspectives and give directions to new annotation strategies and performance evaluation protocols aiming to solve current issues hampering the incorporation of cheminformatics annotation approaches in regular eco-exposome annotation workflows.     

Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning

Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental times. We present a proof‐of‐concept of the application of deep learning and neural networks for high‐quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solely synthetic NMR signals, which lifts the prohibiting demand for a large volume of realistic training data usually required for a deep learning approach.     

Prediction of 5-hydroxytryptamine transporter inhibitors based on machine learning

In patients with depression, the use of 5-HT reuptake inhibitors can improve the condition. Machine learning methods can be used in ligand-based activity prediction processes. In order to predict SERT inhibitors, the SERT inhibitor data from the ChEMBL database was screened and pre-processed. Then 4 machine learning methods (LR, SVM, RF, and KNN) and 4 molecular fingerprints (CDK, Graph, MACCS, and PubChem) were used to build 16 prediction models. The top 5 models of accuracy (Q) in the cross-validation of training set were used to build three different ensemble learning models. In the test1 set, the VOT_CLF3 model had the largest SP (0.871), Q (0.869), AUC (0.919), and MCC (0.728). In the unbalanced test2 set, VOT_CLF3 had the largest SE (0.857), SP (0.867), Q (0.865) and MCC (0.639). VOT_CLF3 was recommended for the virtual screening process of SERT inhibitors. In addition, 12 molecular structural alerts that frequently appear in SERT inhibitors were found (P < 0.05), which provided important reference value for the design work of SERT inhibitors.     

Density Functional Theory as a Data Science

The development of density functional theory (DFT) functionals and physical corrections are reviewed focusing on the physical meanings and the semiempirical parameters from the viewpoint of data science. This review shows that DFT exchange‐correlation functionals have been developed under many strict physical conditions with minimizing the number of the semiempirical parameters, except for some recent functionals. Major physical corrections for exchange‐correlation function‐ als are also shown to have clear physical meanings independent of the functionals, though they inevitably require minimum semiempirical parameters dependent on the functionals combined. We, therefore, interpret that DFT functionals with physical corrections are the most sophisticated target functions that are physically legitimated, even from the viewpoint of data science.