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Chinese Journal of Structural Chemistry 2002年第6期21卷 592-596页

作者： Zheng－TaoXu StephenLee DepartmentofChemistryandChemicalBiology BakerLaboratoryCornellUniversityIthacaNY14853－1301 Authortowhomcorrespondenceshouldbeaddressed

The structure type for the crystal of 4,4'-bis-(2-hydroxy-ethoxyl)-biphenyl 1 has been predicted by using the previously developed interfacial model for small organic molecules. Based on the calculated hydrophobic to hydrophilic volume of 1, this model predicts the crystal structure to be of lamellar or bicontinuous type, which has been confirmed by the X-ray single-crystal structure analysis (C20H26O6, monoclinic, P21/C, a = 16.084(1), b = 6.0103(4), c = 9.6410(7) A, β9 = 103.014(2)°, V= 908.1(1) A3, Z = 2, Dc= 1.325 g/cm3, F(000)=388,μ = 0.097 mm-1, MoKα radiation, λ = 0.71073 A, R = 0.0382 and wR = 0.0882 with I > 2σ(I) for 7121 reflections collected, 1852 unique reflections and 170 parameters). As predicted, the hydrophobic and hydrophilic portions of 1 form in the lamellae. The same interfacial model is applied to other amphilphilic small molecule organic systems for structural type prediction.

关键词： amphiphilic system minimal surface organic crystal structure prediction

structure prediction, ENUMERATION AND WHOLESALE MOLECULAR ORBITAL CALCULATION OF POLYCYCLIC AROMATIC HYDROCARBONS

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Science in China,Ser.B 1986年第11期29卷 1133-1146页

作者：戴乾圜石冰志 Beijing Polytechnic University

Based upon our previous works, a systematic mathematical demonstration of polycyclic aromatic hydrocarbons (PAH) graphs has been carried out in this laboratory. The uniqueness of characteristic number (linear topology notation of PAH), the even number theorem for the discriminating of complete aromaticity for PAH in structure prediction and enumeration, the transformation theorem from the characteristic number to form the adjacency matrix uniquely, the diserote mathematics strategy for the programming of the automatic MO calculation to a whole class of compounds as well as the other aspects have been demonstrated in this paper. In terms of these research, the wholesale molecular orbital calculation (WMO) and the linear notation containing all the topologic information of PAH molecule have been put forward for the first time, so the first example for the structure prediction and enumeration of PAH having truly chemical significance as well as automatic, systematic MO calculation of whole compound class h

关键词： PAH ENUMERATION AND WHOLESALE MOLECULAR ORBITAL CALCULATION OF POLYCYCLIC AROMATIC HYDROCARBONS structure prediction

structure prediction of Membrane Proteins

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Genomics, Proteomics & Bioinformatics 2004年第1期2卷 1-5页

作者： ChunlongZhou YaoZheng YanZhou HangzhouGenomicsInstitute／JamesD.WatsonInstituteofGenomeSciences ZhejiangUniversity／KeyLaboratoryofBioinformaticsofZhejiangProvinceHangzhou310008China CenterforEngineeringandScientificComputation ZhejiangUniversityHangzhou310027China

There is a large gap between the number of membrane protein (MP) sequencesand that of their decoded 3D structures, especially high-resolution structures, due to difficultiesin crystal preparation of MPs. However, detailed knowledge of the 3D structure is required for thefundamental understanding of the function of an MP and the interactions between the protein and itsinhibitors or activators. In this paper, some computational approaches that have been used topredict MP structures are discussed and compared.

关键词： structure prediction membrane proteins

Improving RNA secondary structure prediction using direct coupling analysis

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Chinese Physics B 2020年第7期29卷 104-110页

作者：何小玲王军王剑肖奕 School of Physics Huazhong University of Science and TechnologyWuhan 430074China

Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding *** the last decades,a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered *** we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence *** further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.

关键词： RNA secondary structure structure prediction direct coupling analysis

Computational analysis of apatite-type compounds for band gap engineering: DFT calculations and structure prediction using tetrahedral substitution

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Rare Metals 2021年第12期40卷 3694-3700页

作者： Hai-Kun Liu Li-Bing Liao Yuan-Yuan Zhang Sergey MAksenov Ning Liu Qing-Feng Guo Dina V.Deyneko Tian-Yi Wang Le-Fu Mei Cheng-Hua Sun Science and Technology Innovation Institute Dongguan University of TechnologyDongguan 523808China School of Chemical Engineering and Energy Technology Dongguan University of TechnologyDongguan 523808China Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral MaterialsSchool of Materials Sciences and TechnologyChina University of GeosciencesBeijing 100083China School of Materials Sciences and Technology Dongguan University of TechnologyDongguan 523808China

Mineral apatite compounds have attracted significant interest due to their chemical stability and adjustable hexagonal structure,which makes them suitable as new photovoltaic functional *** band gap of natural apatite is ~5.45 eV,and such a large value limits their applications in the field of catalysis and energy *** this research,we designed a method to narrow the band gap via the tetrahedral substitution effect in apatite-based *** density functional theory(DFT) and experimental investigation of the electronic and optical properties revealed that the continuous incorporation of [MO_(4)]^(4-) tetrahedrons(M=Si,Ge,Sn,and Mn) into the crystal lattice can significantly reduce the band *** particular,this phenomenon was observed when the[MnO_(4)]^(4-) tetrahedron replaces the [PO_(4)]^(4-) tetrahedron because of the formation of a Mn 3 d-derived conduction band minimum(CBM) and interacts with other elements,leading to band broadening and obvious reduction of the band *** approach allowed us to propose a novel scheme in the band gap engineering of apatite-based compounds toward an entire spectral range modification.

关键词： Apatite Density functional theory(DFT) Band gap engineering structure prediction Tetrahedral substitution

Mem Brain: An Easy-to-Use Online Webserver for Transmembrane Protein structure prediction

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Nano-Micro Letters 2018年第1期10卷 12-19页

作者： Xi Yin Jing Yang Feng Xiao Yang Yang Hong-Bin Shen Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Department of Computer Science Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane *** Brain web server is free for academic use and available at ***/bioinf/Mem Brain/.

关键词： Transmembrane a-helices structure prediction Machine learning Contact map prediction Relative accessible surface area

Sequence identification, structure prediction and validation of tannase from Aspergillusniger N5-5

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Chinese Chemical Letters 2016年第7期27卷 1087-1090页

作者： Shuai Zhang Feng-Chao Cui Yong Cao Yun-Qi Li College of Food Science South China Agricultural University College of Chemistry and Chemical Engineering Zhaoqing University Key Laboratory of Synthetic Rubber Changchun Institute of Applied Chemistry Chinese Academy of Sciences

Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry *** until now,the 3-D structures of fungi tannases have not been *** protein sequence deduced from the cDNA sequence obtained using RT-PCR amplification was identified as tannase through sequence alignment and phylogenetic *** models based on the tannase sequence were collected using I-TASSER,and the model with the best match to the surface charge density-pH titration profile was selected as the final structure for tannase from Aspergillusniger *** work provides an effective method for protein structure *** structure constructed in this work should be very important to understand the enzyme bioactivities and further developments of fungi tannases.

关键词： Aspergillusniger N5-5 Sequence identification structure prediction Surface charge density Tannase Zeta potential

The 3D structure prediction of TAS2R38 bitter receptors bound to the agonists phenylthiocarbamide（PTC） and Propylthiouracil（PROP）

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The 3D structure prediction of TAS2R38 bitter receptors boun...

A novel method for atomization energy prediction based on natural-parameter network

第十一届全国计算（机）化学学术会议

作者：谭君 Key Laboratory of Biorheological Science and Technology Ministry of EducationBioengineering CollegeChongqing UniversityChongqing400030China Materials and Process Simulation Center（MC139-74） California Institute of Technology1200 E.California Blvd.PasadenaCA 91125USA

＜正＞TAS2R38 bitter taste receptors are seven-transmembrane（TM） domain G protein-coupled receptors（GPCRs） that can respond to bitter compounds such as Phenylthiocarbamide（PTC）.They are expressed not only in the gustatory system but also in subsets of cells within the mammalian gastrointestinal tract,where they mediate nutrient assimilation and endocrine *** binding of the agonist PTC to the receptors can result in the activation of bitter taste receptors, which stimulates ghrelin secretion,modulates endogenous ghrelin levels and alters glucose and insulin homeostasis[1-3].

关键词： TAS2R38 bitter taste receptors GPCRs structure prediction phenylthiocarbamide and Propylthiouracil Docking

来源： cnki会议评论

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Chinese Chemical Letters 2024年第1期35卷 505-509页

作者： Chaoqin Chu Qinkun Xiao Chaozheng He Chen Chen Lu Li Junyan Zhao Jinzhou Zheng Yinhuan Zhang School of Mechanical and Electrical Engineering Xi’an Technological UniversityXi’an 710021China School of Electrical and Information Engineering Xi’an Technological UniversityXi’an 710021China School of Materials Science and Chemical Engineering Xi’an Technological UniversityXi’an 710021China

Atomization energy(AE)is an important indicator for measuring material stability and reactivity,which refers to the energy change when a polyatomic molecule decomposes into its constituent *** AE based on the structural information of molecules has been a focus of researchers,but existing methods have limitations such as being time-consuming or requiring complex preprocessing and large amounts of training *** learning(DL),a new branch of machine learning(ML),has shown promise in learning internal rules and hierarchical representations of sample data,making it a potential solution for AE *** address this problem,we propose a natural-parameter network(NPN)approach for AE *** method establishes a clearer statistical interpretation of the relationship between the network’s output and the given *** use the Coulomb matrix(CM)method to represent each compound as a structural information ***,we also designed an end-to-end predictive *** results demonstrate that our method achieves excellent performance on the QM7 and BC2P datasets,and the mean absolute error(MAE)obtained on the QM7 test set ranges from 0.2 kcal/mol to 3 kcal/*** optimal result of our method is approximately an order of magnitude higher than the accuracy of 3 kcal/mol in published ***,our approach significantly accelerates the prediction ***,this study presents a promising approach to accelerate the process of predicting structures using DL,and provides a valuable contribution to the field of chemical energy prediction.

关键词： structure prediction Atomization energy Deep learning Coulomb matrix NPN End-to-end

structure search of two-dimensional systems using CALYPSO methodology

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Frontiers of physics 2022年第2期17卷 121-134页

作者： Pengyue Gao Bo Gao Shaohua Lu Hanyu Liu Jian Lv Yanchao Wang Yanming Ma International Center for Computational Method&Software College of PhysicsJilin UniversityChangchun 130012China State Key Laboratory of Superhard Materials College of PhysicsJilin UniversityChangchun 130012China Center for Green Research on Energy and Environmental Materials(GREEN)and International Center for Materials Nanoarchitectonics(MANA) National Institute for Materials Science1-1 NamikiTsukubaIbaraki 305-0044Japan College of Materials Science and Engineering Zhejiang University of TechnologyHangzhou 310014China International Center of Future Science Jilin UniversityChangchun 130012China

The dimensionality of structures allows materials to be classified into zero-, one-, two-, and threedimensional systems. Two-dimensional (2D) systems have attracted a great deal of attention andtypically include surfaces, interfaces, and layered materials. Due to their varied properties, 2D systemshold promise for applications such as electronics, optoelectronics, magnetronics, and *** design of 2D systems is an area of intensive research because of the rapid development of abinitio structure-searching methods. In this paper, we highlight recent research progress on acceleratingthe design of 2D systems using the CALYPSO methodology. Challenges and perspectives for futuredevelopments in 2D structure prediction methods are also presented.

关键词： two-dimensional(2D)systems CALYPSO structure prediction