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Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 页码: 135
Authors:  Wang, C;  Wei, Y;  Zhang, HC;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB
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TERTIARY STRUCTURES  FRAGMENTS  
DCA for genome-wide epistasis analysis: the statistical genetics perspective 期刊论文
PHYSICAL BIOLOGY, 2019, 卷号: 16, 期号: 2, 页码: 26002
Authors:  Gao, CY;  Cecconi, F;  Vulpiani, A;  Zhou, HJ;  Aurell, E
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DIRECT-COUPLING ANALYSIS  PROTEIN-STRUCTURE  CONTACTS  HIV  IDENTIFICATION  RECOMBINATION  LINKAGE  LANDSCAPE  INFERENCE  MODEL  
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018, 卷号: 86, 页码: 136-151
Authors:  Zhang, CX;  Mortuza, SM;  He, BJ;  Wang, YT;  Zhang, Y
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PROTEIN-STRUCTURE PREDICTION  RESIDUE CONTACTS  SEQUENCE  ALIGNMENTS  ACCURACY  NETWORKS  ROLL  
Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder 期刊论文
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2018, 卷号: 36, 期号: 9, 页码: 2331-2341
Authors:  Faraggi, E;  Dunker, AK;  Sussman, JL;  Kloczkowski, A
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BACKBONE TORSION ANGLES  MAJOR URINARY PROTEIN  INTRINSIC DISORDER  STRUCTURE PREDICTION  SECONDARY STRUCTURE  CRYSTAL-STRUCTURE  DYNAMICS  DIFFRACTION  CRYSTALLOGRAPHY  RECOGNITION  
NeBcon: protein contact map prediction using neural network training coupled with naiive Bayes classifiers 期刊论文
BIOINFORMATICS, 2017, 卷号: 33, 期号: 15, 页码: 2296-2306
Authors:  He, BJ;  Mortuza, SM;  Wang, YT;  Shen, HB;  Zhang, Y;  Zhang, Y (reprint author), Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA.;  Zhang, Y (reprint author), Univ Michigan, Dept Biol Chem, Ann Arbor, MI 48109 USA.
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A novel 3-D bio-microfluidic system mimicking in vivo heterogeneous tumour microstructures reveals complex tumour-stroma interactions 期刊论文
LAB ON A CHIP, 2017, 卷号: 17, 期号: 16, 页码: 2852-2860
Authors:  Fan, QH;  Liu, RC;  Jiao, Y;  Tian, CX;  Farrell, JD;  Diao, WW;  Wang, XC;  Zhang, FR;  Yuan, W;  Han, HB;  Chen, JF;  Yang, Y;  Zhang, XX;  Ye, FF;  Li, M;  Ouyang, ZC;  Liu, LY;  Ye, FF (reprint author), Chinese Acad Sci, Beijing Natl Lab Condensed Matter Phys, Inst Phys, Beijing 100190, Peoples R China.;  Ye, FF (reprint author), Chinese Acad Sci, CAS Key Lab Soft Matter Phys, Inst Phys, Beijing 100190, Peoples R China.;  Liu, LY (reprint author), Chongqing Univ, Coll Phys, Chongqing 401331, Peoples R China.;  Ouyang, ZC (reprint author), Chinese Acad Sci, Inst Theoret Phys, CAS Key Lab Theoret Phys, Beijing 100190, Peoples R China.;  Ouyang, ZC (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.
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Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity 期刊论文
PLOS COMPUTATIONAL BIOLOGY, 2017, 卷号: 13, 期号: 2, 页码: e1005384
Authors:  Yang, DP;  Zhou, HJ;  Zhou, CS;  Zhou, CS (reprint author), Hong Kong Baptist Univ, Dept Phys, Kowloon Tong, Hong Kong, Peoples R China.;  Zhou, CS (reprint author), Hong Kong Baptist Univ, Ctr Nonlinear Studies, Kowloon Tong, Hong Kong, Peoples R China.;  Zhou, CS (reprint author), Hong Kong Baptist Univ, Beijing Hong Kong Singapore Joint Ctr Nonlinear &, Inst Computat & Theoret Studies, Kowloon Tong, Hong Kong, Peoples R China.;  Yang, DP (reprint author), Univ Sydney, Sch Phys, Sydney, NSW, Australia.;  Zhou, CS (reprint author), Beijing Computat Sci Res Ctr, Beijing, Peoples R China.;  Zhou, CS (reprint author), Virtual Univ, HKBU Inst Res & Continuing Educ, Res Ctr, Pk Bldg,South Area Hitech Ind Pk, Shenzhen, Peoples R China.
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Improving prediction of burial state of residues by exploiting correlation among residues 期刊论文
BMC BIOINFORMATICS, 2017, 卷号: 18, 页码: 70
Authors:  Gong, HE;  Zhang, HC;  Zhu, JW;  Wang, C;  Sun, SW;  Zheng, WM;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Proc, Beijing 100190, Peoples R China.;  Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
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Protein Structure  Burial States Of Residue  Conditional Random Field  Residue Correlation  
Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2017, 卷号: 85, 期号: 6, 页码: 1002-1007
Authors:  Wu, SG;  Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
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Molecular Dynamics Simulation  T7 Rna Polymerase  Magnesium Ion  Transcription Mechanism  Free Energy  
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts 期刊论文
BIOINFORMATICS, 2017, 卷号: 33, 期号: 23, 页码: 3749-3757
Authors:  Zhu, JW;  Zhang, HC;  Li, SC;  Wang, C;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China.;  Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
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