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LIST
OF PUBLICATIONS
Publications
in the Area of Computational Biology and Drug Design
- The database and bioinformatics studies of probiotics. L. Tao, B. Wang, Y. Zhong, S. H. Pow, X. Zeng, C. Qin, P. Zhang, S. Chen, W. He, Y. Tan, H. Liu, Y. Jiang, W. Chen, Y. Z. Chen. J. Agric. Food Chem. doi: 10.1021/acs.jafc.7b01815. (2017).
- Novel multi-substituted benzyl acridone derivatives as survivin inhibitors for hepatocellular carcinoma treatment. B. Zhang, N. Wang, C.L. Zhang, C.M. Gao, W. Zhang, K. Chen, W.B. Wu, Y.Z. Chen, C.Y. Tan, F. Liu, Y.Y. Jiang. Eur J Med Chem. 129:337-348 (2017).
- Design, synthesis and anticancer potential of NSC-319745 hydroxamic acid derivatives as DNMT and HDAC inhibitors. Z.G. Yuan, Q.S. Sun, D. Lia, S.S. Miao, S.P. Chen, L. Song, C.M. Gao, Y.Z. Chen, C.Y. Tan, Y.Y. Jiang Eur J Med Chem. 134:281-292 (2017).
- Differentiating Physicochemical Properties between Addictive and Nonaddictive ADHD Drugs Revealed by Molecular Dynamics Simulation Studies. P.P. Wang, X.Y. Zhang, T.T. Fu, S. Li, B. Li, W.W. Xue, X.J. Yao, Y.Z. Chen, F. Zhu. ACS Chem Neurosci. 8(6):1416-1428 (2017).
- NOREVA: normalization and evaluation of MS-based metabolomics data. B. Li, J. Tang, Q.X. Yang, S. Li, X.J. Cui, Y.H. Li, Y.Z. Chen, W.W. Xue, X.F. Li, F. Zhu. Nucleic Acids Res. doi:10.1093/nar/gkx449 (2017).
- Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway. L. Huang, Y. Y. Jiang, Y. Z. Chen. Sci Rep. 7:40752 (2017).
- HEROD: a human ethnic and regional specific omics database. X. Zeng, L. Tao, P. Zhang, C. Qin, S. Chen, W. He, Y. Tan, H. X. Liu, S. Y. Yang, Z. Chen, Y. Y. Jiang, Y. Z. Chen. Bioinformatics. doi: 10.1093/bioinformatics/btx340 (2017).
- Discovery of novel dual VEGFR2 and Src inhibitors using a multistep virtual screening approach. S.Y. Chen, C. Qin, JE. Sin, X. Yang, L. Tao, X. Zeng, P. Zhang, CM. Gao, Y.Y. Jiang, C. Zhang, Y.Z. Chen, W.K. Chui. Future Med Chem. 9(1):7-24 (2017).
- PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks. P. Zhang, L. Tao, X. Zeng, C. Qin, S.Y. Chen, F. Zhu, S.Y. Yang, Z.R. Li, W.P. Chen, Y.Z. Chen. J Mol Biol. pii:S0022-2836(16)30428-4. (2016).
- A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. P. Zhang, L. Tao, X. Zeng, C. Qin, S.Y. Chen, F. Zhu, Z.R. Li, Y.Y. Jiang, W.P. Chen, Y.Z. Chen. Brief Bioinform. pii: bbw071 (2016).
- SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. Y.H. Li, J.Y. Xu, L. Tao, X.F. Li, S. Li, X. Zeng, S.Y. Chen, P. Zhang, C. Qin, C. Zhang, Z. Chen, F. Zhu, Y.Z. Chen. PLoS One.11(8):e0155290 (2016).
- Towards cheminformatics-based estimation of drug therapeutic index: Predicting the protective index of anticonvulsants using a new quantitative structure-index relationship approach. S.Y. Chen, P. Zhang, X. Liu, Q. Chu, L. Tao, C. Zhang, S.Y. Yang, Y.Z. Chen, W.K. Chui. J. Mol. Graph. Model. 67:102-110 (2016).
- Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study. W. Xue, P. Wang, B. Li, Y. Li, X. Xu, F. Yang, X. Yao, Y.Z. Chen, F. Xu, F. Zhu. Phys Chem Chem Phys. 18(4):3260-71 (2016).
- Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. H. Yang, C. Qin, Y.H. Li, L. Tao, J. Zhou, C.Y. Yu, F. Xu, Z. Chen, F. Zhu, Y.Z. Chen. Nucleic Acids Res. 44(D1):D1069-74 (2016).
- The Assessment of the Readiness of Molecular Biomarker-Based Mobile Health Technologies for Healthcare Applications. C. Qin, L. Tao, Y.H. Pang, C. Zhang, S.Y. Chen, P. Zhang, Y. Tan, Y.Y. Jiang, Y.Z. Chen. Sci Rep. 5:17854 (2015).
- Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs. L. Tao, F. Zhu, F. Xu, Z. Chen, Y.Y. Jiang, Y.Z. Chen. Pharmacol Res. 102:123-131 (2015).
- Fluorescence array-based sensing of metal ions using conjugated polyelectrolytes. Y. Wu, Y. Tan, J. Wu, S. Chen, Y.Z. Chen, X. Zhou, Y. Jiang and C. Tan. ACS Appl Mater Interfaces. 7(12):6882-8 (2015).
- Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools. L. Tao, P. Zhang, C. Qin, S.Y. Chen, C. Zhang, Z. Chen, F. Zhu, S.Y. Yang, Y.Q. Wei, Y.Z. Chen. Adv Drug Deliv Rev. 86:83-100 (2015).
- Physicochemical profiles of the marketed agrochemicals and clues for agrochemical lead discovery and screening library development. H.B. Rao, C.X. Huangfu, Y.Y. Wang, X.X. Wang, T.S. Tang, X.Y. Zeng, Z.R. Li and Y.Z. Chen. Mol Inform. 34(5):331-338 (2015).
- A preclinical evaluation of SKLB261, a multikinase inhibitor of EGFR/Src/VEGFR2, as a therapeutic agent against pancreatic cancer. Y. Pan, M. Zheng, L. Zhong, J. Yang, S. Zhou, Y. Qin, R. Xiang, Y.Z. Chen and S.Y. Yang. Mol Cancer Ther. 14(2):407-18 (2015).
- Clustered Distribution of Natural Product Leads of Drugs in the Chemical Space as Influenced by the Privileged Target-Sites. L. Tao, F. Zhu, C. Qin, C. Zhang, S.Y. Chen, P. Zhang, C.L. Zhang, C.Y. Tan, C.M. Gao, Z. Chen, Y.Y. Jiang and Y.Z. Chen. Sci Rep. 5:9325 (2015).
- CFam: A Chemical Families Database Based on Iterative Selection of Functional Seeds and Seed-Directed Compound Clustering. C. Zhang, L. Tao, C. Qin, P. Zhang, S.Y. Chen, X. Zeng, F. Xu, Z. Chen, S.Y. Yang and Y.Z. Chen. Nucleic Acids Res. 43:D558-65 (2015).
- Nature's contribution to today's pharmacopeia. L. Tao, F. Zhu, C. Qin, C. Zhang, F. Xu, C.Y. Tan, Y.Y. Jiang, Y.Z. Chen. Nat Biotechnol. 32(10):979-80 (2014).
- Optimization of culture conditions of Bacillus subtilis natto and preparation of freeze-dried powders as a potentially novel antithrombotic probiotic. M.F. He, K.J. Tang, B.H. Wang, M.H. Qu, L.P. Lin, Y.Z. Chen and W.P. Chen. J. Pure Appl Microbiology. 8(2):1619-1625 (2014).
- A Resource for Facilitating the Development of Tools in the Education and Implementation of Genomics-Informed Personalized Medicine. C. Zhang, C. Qin, L. Tao, F. Zhu, S.Y. Chen, P. Zhang, S.Y. Yang, Y. Q. Wei, Y.Z. Chen. Clin Pharmacol Ther. 95:590-591(2014).
- Therapeutic target database update 2014: a resource for targeted therapeutics. C. Qin, C. Zhang, F. Zhu, F. Xu, S.Y. Chen, P. Zhang, Y.H. Li, S.Y. Yang, Y.Q. Wei, L. Tao and Y.Z. Chen. Nucleic Acids Res. 42(1):D1118-23 (2014).
- Exploration of N-(2-aminoethyl)piperidine-4-carboxamide as a potential scaffold for development of VEGFR-2, ERK-2 and Abl-1 multikinase inhibitor. F. Jin, D. Gao, Q. Wu, F. Liu, Y.Z. Chen, C. Tan and Y. Jiang Bioorg Med Chem. 21(18):5694-706 (2013).
- Quantitative structure-activity relationship study of influenza virus neuraminidase A/PR/8/34 (H1N1) inhibitors by genetic algorithm feature selection and support vector regression. Y. Cong, B.K. Li, X.G. Yang, Y. Xue, Y.Z. Chen and Y. Zeng Chemometr. Intell. Lab. 127:35-42 (2013).
- In silico prediction of spleen tyrosine kinase inhibitors using machine learning approaches and an optimized molecular descriptor subset generated by recursive feature elimination method. B.K. Li, Y. Cong, X.G. Yang, Y. Xue and Y.Z. Chen. Comput Biol Med. 43(4):395-404 (2013).
- Exploration of 1-(3-chloro-4-(4-oxo-4H-chromen-2-yl)phenyl)-3-phenylurea derivatives as selective dual inhibitors of Raf1 and JNK1 kinases for anti-tumor treatment. F. Jin, D. Gao, C. Zhang, F. Liu, B. Chu, Y. Chen, Y.Z. Chen, C. Tan and Y. Jiang. Bioorg Med Chem. 21(3):824-831 (2013).
- Predicting Targeted Polypharmacology for Drug Repositioning and Multi-Target Drug Discovery. X. Liu, F. Zhu, X.H. Ma, Z. Shi, S.Y. Yang, Y.Q. Wei and Y.Z. Chen. Curr Med Chem. 20(13):1646-1661 (2013).
- Toxicogenomic analysis suggests chemical-induced sexual dimorphism in the expression of metabolic genes in zebrafish liver. X. Zhang, C.Y. Ung, S.H. Lam, J. Ma, Y.Z. Chen, L. Zhang, Z. Gong and B. Li. PLoS One. 7(12):e51971 (2012).
- Development and experimental test of support vector machines virtual screening method for searching Src inhibitors from large compound libraries. B.C. Han, X.H. Ma, R.Y. Zhao, J.X. Zhang, X.N. Wei, X.H. Liu, X. Liu, C.L. Zhang, C.Y. Tan, Y.Y. Jiang and Y.Z. Chen. Chem Cent J. 6:139 (2012).
- A global characterization and identification of multifunctional enzymes. X.Y. Cheng, W.J. Huang, S.C. Hu, H.L. Zhang, H. Wang, J.X. Zhang, H.H. Lin, Y.Z. Chen, Q. Zou and Z.L. Ji. PLoS ONE. 7(6):e38979 (2012).
- Prediction of human major histocompatibility complex class II binding peptides by continuous kernel discrimination method. J. He, G. Yang, H. Rao, Z. Li, X. Ding and Y.Z. Chen. Artif Intell Med. 55(2):107-15 (2012).
- Synthesis and Cytotoxic Activity of Some Novel N-Pyridinyl-2-(6-phenylimidazo[2,1-b]thiazol-3-yl)acetamide Derivatives. H. Ding, Z. Chen, C. Zhang, T. Xin, Y. Wang, H. Song, Y. Jiang, Y.Z. Chen, Y. Xu and C. Tan C. Molecules. 17(4):4703-16 (2012).
- Neighbor communities in drug combination networks characterize synergistic effect. J. Zou, P. Ji, Y.L. Zhao, L.L. Li, Y.Q. Wei, Y.Z. Chen and S.Y. Yang. Mol Biosyst. 8(12):3185-96 (2012).
- The interprotein scoring noises in glide docking scores. W. Wang, X. Zhou, W. He, Y. Fan, Y.Z. Chen and X. Chen. Poteins. 80(1):169-83 (2012).
- MicrobPad MD: Microbial Pathogen Diagnostic Methods Database. B.C. Han, X.N. Wei, J.X. Zhang, N.Q.T. Truong, C.L. Westgate, R.Y. Zhao and Y.Z. Chen. Infect. Genet. Evol. 13:261-6 (2012).
- What does it take to synergistically combine sub-potent natural products into drug-level potent combinations? C. Qin, K.L. Tan, C.L. Zhang, C.Y. Tan, Y.Z. Chen and Y.Y. Jiang. PLoS ONE. 7(11):e49969 (2012).
- Virtual screening methods as tools for drug lead discovery from large chemical libraries. X.H. Ma, F. Zhu, X. Liu, Z. Shi, J.X. Zhang, S.Y. Yang, Y.Q. Wei and Y.Z. Chen. Curr Med Chem.. 19(32):5562-71 (2012).
- In silico prediction of adverse drug reactions and toxicities based on structural, biological and clinical data. X. Liu, Z. She, Y. Xue, Z.R. Li, S.Y. Yang and Y.Z. Chen. Current Drug Safety. 7(3):225-37 (2012).
- Drug Discovery Prospect from Untapped Species: Indications from Approved Natural Product Drugs. F. Zhu, X.H. Ma, C. Qin, L. Tao, X. Liu, Z. Shi, C.L. Zhang, C.Y. Tan, Y.Y. Jiang and Y.Z. Chen. PLoS ONE. 7(7):e39782 (2012).
- Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors. J.X. Zhang, J. Jia, F. Zhu, X.H. Ma, B.C. Han, X.N. Wei, C.Y. Tan, Y.Y. Jiang and Y.Z. Chen. Mol. BioSyst. Advance Article, 8(10):2645-56 (2012).
- A two-step Target Binding and Selectivity Support Vector Machines Approach for Virtual Screening of Dopamine Receptor Subtype-selective Ligands. J.X. Zhang, B.C. Han, X.N. Wei, C.Y. Tan, Y.Z. Chen and Y.Y. Jiang. PLoS ONE. 7(6):e39076 (2012).
- Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods. H.B. Rao, X.Y. Zeng, Y.Y. Wang, H. He, F. Zhu, Z.R. Li and Y.Z. Chen. Mol. Simul. 38(4):259-273 (2012)
- Therapeutic Target Database Update 2012: A Resource for Facilitating Target-Oriented Drug Discovery. F. Zhu, Z. Shi, C. Qin, L. Tao, X. Liu, F. Xu, L. Zhang, Y. Song, X.H. Liu, J.X. Zhang, B.C. Han, P. Zhang and Y.Z. Chen. Nucleic Acids Res. 40(D1):D1128-D1136 (2012). Pubmed
- Combinatorial Support Vector Machines Approach for Virtual Screening of Selective Multi-Target Serotonin Reuptake Inhibitors from Large Compound Libraries.
Z. Shi, X.H. Ma, C. Qin, J. Jia, Y.Y. Jiang, C.Y. Tan, Y.Z. Chen.
J Mol Graph Model. 32:49-66 (2012).
- Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits.
Kun Yan, Yu-Zong Chen, Jongyoon Han, Gui-Rong Liu, Jian-Sheng Wang, Nicoloas G. Hadjiconstantinou.
Microfluid Nanofluid. 12(1-4):157-163 (2012).
- Simulating
EGFR-ERK Signaling Control by Scaffold Proteins KSR and MP1 Reveals
Differential Ligand-Sensitivity Co-Regulated by Cbl-CIN85 and Endophilin.
Huang
L, Pan CQ, Li B, Tucker-Kellogg L, Tidor B, Yuzong Chen, Boon Chuan
Low.
PLoS
ONE. 6(8):e22933 (2011).
- An
Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated
Signalling in Endothelial Permeability. Wei
XN, Han BC, Zhang JX, Liu XH, Tan CY, Jiang YY, Low BC, Tidor B, Chen
YZ.
BMC Syst Biol.
Jul 15;5(1):112 (2011). Pubmed
- Discovery
of benzimidazole derivatives as novel multi-target EGFR, VEGFR-2 and
PDGFR kinase inhibitors.
Li Y, Tan C, Gao C, Zhang C, Luan X, Chen X, Liu H, Chen Y and Jiang
Y. Bioorg
Med Chem. 19(15):4529-35 (2011). Pubmed
- Clustered
patterns of species origins of nature-derived drugs and clues for
future bioprospecting.
F. Zhu, C. Qin, L. Tao, X. Liu, Z. Shi, X.H. Ma, J. Jia, Y. Tan, C.
Cui, J.S. Lin, C.Y. Tan, Y.Y. Jiang and Y.Z. Chen. PNAS.
108(31):12943-8 (2011). Pubmed
- Exploration
of acridine scaffold as a potentially interesting scaffold for discovering
novel multi-target VEGFR-2 and Src kinase inhibitors.
X. Luan, C. Gao, N. Zhang, Y.Z. Chen, Q. Sun, C.Y. Tan, H. Liu, Y.
Jin and Y.Y. Jiang. Bioorg
Med Chem. 19(11):3312-9 (2011). Pubmed
- The
Therapeutic Target Database: an internet resource for the primary
targets of approved, clinical trial and experimental drugs.
X. Liu, F. Zhu, X.H. Ma, L, Tao, J.X. Zhang, S.Y. Yang, Y.C. Wei and
Y.Z. Chen. Expert
Opin Ther Targets. 15(8):903-12 (2011). Pubmed
- Effect
of Training Data Size and Noise Level on Support Vector Machines Virtual
Screening of Genotoxic Agents from Large Compound Libraries.
Pankaj Kumar, X.H. Ma, X.H. Liu, J. Jia, B.C. Han, Y. Xue, Z.R. Li,
S.Y. Yang, Y.C. Wei and Y.Z. Chen. J
Comput Aided Mol Des. 25(5):455-67 (2011).
- Exploration
of (S)-3-aminopyrrolidine as a potentially interesting scaffold for
discovery of novel Abl and PI3K dual inhibitors.
C.L. Zhang, C.Y. Tan, X.Y. Zu, X. Zhai, F. Liu, B.Z. Chu, X.H. Ma,
Y.Z. Chen, P. Gong, Y.Y. Jiang. Eur
J Med Chem. 46(4), 1404-1414 (2011). Pubmed
- Update
of PROFEAT: a web server for computing structural and physicochemical
features of proteins and peptides from amino acid sequence. H.B.
Rao, F. Zhu, G.B. Yang, Z.R. Li, and Y.Z. Chen. Nucleic
Acids Res. 39(Database issue):W385-90(2011). Pubmed
- Dispersive
Transport of Biomolecules in Periodic Energy Landscapes with application
to Nanofilter Sieving Arrays. Li,
Z. R., G. R. Liu, N. G. Hadjiconstantinou, J. Han, J. S. Wang, and
Y. Z. Chen. Electrophoresis
32, 506-517 (2011). Pubmed
- Classification
Models for Acetylcholinesterase Inhibitors Based on Machine Learning
Methods.
Yang GB, Li ZR , Rao HB, Li XY, Chen YZ. Acta
Physico-Chimica Sinica Volume: 26 Issue: 12 Pages: 3351-3359 (2010)
- HIT:
linking herbal active ingredients to targets.
H. Ye, L. Ye, H. Kang, D.F. Zhang, L. Tao, K.L. Tang, X.P. Liu X,
R.X. Zhu, Q. Liu, Y.Z. Chen, Y.X. Li and Z.W. Cao. Nucleic
Acids Res. 39 (suppl_1): D1055-D1059 (2011).
Pubmed
- Virtual
screening of selective multi-target kinase inhibitors by combinatorial
support vector machines.
X.H. Ma, R. Wang, C.Y. Tan, Y.Y. Jiang, T. Lu, H.B. Rao, X.Y. Li,
M.L. Go, B.C. Low and Y.Z. Chen.Mol.
Pharmaceutics. 7(5):1545-60(2010).
Pubmed
- An
insight into the opening path to semi-open conformation of HIV-1 protease
by molecular dynamics simulation.
T. Lu, Y.Z. Chen. and X.Y. Li. AIDS.
24(8):1121-5(2010).
Pubmed
- In
Silico Prediction and Screening of gamma-Secretase Inhibitors by Molecular
Descriptors and Machine Learning Methods.
X.G. Yang, W. Lv, Y.Z. Chen. and Y. Xue.J
Comput Chem.
31(6):1249-58(2010).
Pubmed
- Identifying
Novel Type ZBGs and Non-hydroxamate HDAC Inhibitors Through a SVM
Based Virtual Screening Approach.
X.H. Liu, H.Y. Song, J.X. Zhang, B.C. Han, X.N. Wei, X.H. Ma, W.K.
Chui, Y.Z. Chen. Mol
Inf. 29(5):
407-20(2010)
- In-Silico
Approaches to Multi-Target Drug Discovery.
H.X. Ma, Z. Shi, C.Y. Tan, Y.Y. Jiang, M.L. Go, B.C. Low and Y.Z.
Chen.Pharm
Res.
27(5):2101-10(2010). Pubmed
- Virtual
Screening Prediction of New Potential Organocatalysts for Direct Aldol
Reactions.
X.H. Liu, H.Y. Song, H.X. Ma, M.J. Lear and Y.Z. Chen. J
Mol Catal A: Chem. 319:114-118(2010).
- Update
of TTD: Therapeutic Target Database.
F.
Zhu, B.C. Han, P. Kumar, X.H. Liu, X.H. Ma, X.N. Wei, L. Huang, Y.F.
Guo, L.Y. Han, C.J. Zheng, Y.Z. Chen. Nucleic
Acids Res.
38(Database issue):D787-91(2010). Pubmed
- Virtual
Screening of Abl Inhibitors from Large Compound Libraries by Support
Vector Machines. X.H.
Liu, X.H. Ma, C.Y. Tan, Y.Y. Jiang, M.L. Go, B.C. Low and Y.Z. Chen.
J
Chem Info Model.
49(9):2101-10(2009).
Pubmed
- Prediction
of Antibacterial Compounds by Machine Learning Approaches.
X.G.
Yang, D. Chen, M. Wang, Y. Xue and Y.Z. Chen. J
Comput Chem.
30(8):1202-11(2009).
Pubmed
- Identification
of Small Molecule Aggregators from Large Compound Libraries by Support
Vector Machines. H.B.
Rao, Z.R. Li, X.Y. Li, X.H. Ma, C.Y. Ung, H. Li, X.H. Liu and Y.Z.
Chen. J
Comput Chem. 2010 Mar;31(4):752-63.
- What
are next generation innovative therapeutic targets? Clues from genetic,
structural, physicochemical and system profile of successful targets.
F.
Zhu, L.Y. Han, C.J. Zheng, B. Xie, M.T. Tammi, S.Y. Yang, Y.Q. Wei
and Y.Z. Chen. J
Pharmacol Exp Ther. 330(1):304-15(2009).
- Synergistic
therapeutic actions of herbal ingredients and their mechanisms from
molecular interaction and network perspectives X.
H. Ma, C.J. Zheng, L.Y. Han, B. Xie, J. Jia, Z.W. Cao, Y.X. Li and
Y. Z. Chen. Drug
Discov Today.
14:579-588(2009).
- Pathway
sensitivity analysis for detecting pro-proliferation activities of
oncogenes and tumor suppressors of EGFR-ERK pathway at altered protein
levels H.
Li, C. Y. Ung, X. H. Ma, X. H. Liu, B. W. Li, B. C. Low and Y. Z.
Chen. Cancer.
15(18):4246-4263(2009).
- Genome-Scale
Search of Tumor-Specific Antigens by Collective Analysis of Mutations,
Expressions and T-Cell Recognition. J.
Jia, Cui. J. , X. H. Liu, J. H. Han, S. Y. Yang, Y. Q. Wei, and Y.
Z. Chen. Mol.
Immunol.
46:1824-1829(2009).
- Simulation
of Crosstalk between Small GTPase RhoA and EGFR-ERK Signaling Pathway
via MEKK1. H.
Li, C. Y. Ung, X. H. Ma, B. W. Li, B. C. Low, Z. W. Cao and Y. Z.
Chen.Bioinformatics.
25(3):358-64(2009).
Pubmed
- Update
of KDBI: Kinetic Data of Bio-molecular Interaction Database. P.
Kumar, Z.L. Ji, B.C. Han, Z. Shi, J. Jia, Y.P, Wang, Y.T. Zhang, L.
Liang, and Y. Z. Chen. Nucleic
Acids Res. 37(Database
issue): D636-41(2009).
Pubmed
- Comparative
analysis of machine learning methods in ligand-based virtual screening
of large compound libraries. X.H.
Ma, J. Jia, F. Zhu, Y. Xue, Z.R. Li and Y.Z. Chen. Comb.
Chem. High Throughput Screen.
12(4):344-357(2009).
- Simulation
of DNA Electrophoresis in Systems of Large Number of Solvent Particles
by Coarse-Grained Hybrid Molecular Dynamics Approach. R.
Wang, J.S. Wang, G.R. Liu, J.Y. Han, N.G. Hadjiconstantinou and Y.
Z. Chen. J
Comput Chem. 30(4):505-13(2009).
Pubmed
- Mechanisms
of drug combinations from interaction and network perspectives
J. Jia, F. Zhu, X.H. Ma, Z.W. Cao, Y.X. Li and
Y.Z. Chen. Nat.
Rev. Drug Discov., 8(2):111-28(2009).
Pubmed
- Trends
in the Exploration of Anticancer Targets and Strategies in Enhancing
the Efficacy of Drug Targeting. F.
Zhu, C.J. Zheng, L.Y. Han, B. Xie, J. Jia, X. Liu, M.T. Tammi, S.Y.
Yang, Y.Q. Wei and Y.Z. Chen. Curr
Mol Pharmacol. 1(3):213-232(2008).
- Simulation
of the Regulation of EGFR Endocytosis and EGFR-ERK Signaling by Endophilin-Mediated
RhoA-EGFR Crosstalk. C.Y.
Ung, H. Li, X.H. Ma, J. Jia, B.W. Li, B.C. Low and Y.Z. Chen.FEBS
Lett. 582:2283-2290 (2008).Pubmed
- Evaluation
of Virtual Screening Performance of Support Vector Machines Trained
by Sparsely Distributed Active Compounds. X.H.
Ma, R. Wang, S.Y. Yang, Z.R. Li, Y. Xue, Y.Q. Wei, B.C. Low and Y.
Z. Chen.J
Chem Inf Model. 48(6):1227-1237 (2008).
Pubmed
- A support vector
machines approach for virtual screening of active compounds of single
and multiple mechanisms from large libraries at an improved hit-rate
and enrichment factor. L.Y.
Han, X.H. Ma, H.H. Lin, J. Jia, F. Zhu, Y. Xue, Z.R. Li, Z.W. Cao,
Z.L. Ji, Y.Z. Chen.
J
Mol Graph Mod. 26(8):1276-1286 (2008)
Pubmed
- Prediction
of Antibiotic Resistance Proteins from Sequence Derived Properties
Irrespective of Sequence Similarity. H.L.
Zhang, H.H. Lin, L. Tao, X.H. Ma, J.L. Dai, J.Jia, Z.W. Cao.Int
J Antimicrob Agents. 32(3):221-226 (2008).
Pubmed
- Advances
in Machine Learning Prediction of Toxicological Properties and Adverse
Drug Reactions of Pharmaceutical Agents. X.H.
Ma, R. Wang, Y. Xue, Z.R. Li, S.Y. Yang, Y.Q. Wei and Y.Z. Chen.Curr
Drug Saf. 3(2):100-114 (2008).
Pubmed
- Homology-Free
Prediction of Functional Class of Proteins and Peptides by Support
Vector Machines. F.
Zhu, L.Y. Han, X. Chen, H.H. Lin, S. Ong, B. Xie, H.L. Zhang, Y.Z.
Chen. Curr.
Protein Pept. Sci.. 9:70-95 (2008).
- Learning
the drug target-likeness of a protein H.
Xu, H.Y. Xu, M. Lin, W. Wang, Z.M. Li, J.J. Huang, Y.Z Chen, X. Chen.Proteomics.
7(23):4255-4263 (2007).Pubmed
- Efficacy
of different protein descriptors in predicting protein functional
families.
S. Ong, H.H. Lin, Y.Z. Chen, Z.R. Li, Z.W. Cao.
BMC Bioinforamtics. 8:300 (2007).Pubmed
- DITOP:
drug-induced toxicity related protein database.
J.X Zhang, W.J. Huang, J.H. Zeng, W.H. Huang, Y. Wang, R. Zhao, B.C.
Han, Q.F. Liu, Y.Z. Chen, Z.L. Ji.
Bioinforamtics. 23(13):1710-1712 (2007).Pubmed
- Formulation
Development of Transdermal Dosage Forms: Quantitative Structure-Activity
Relationship Model for Predicting Activities of Terpenes that Enhance
Drug Penetration Through Human Skin .
L. Kang, C.W. Yap, P.F. Lim, Y.Z. Chen,P.C. Ho, Y.W. Chan, G.P. Wang,
S.Y. Chan.
J Control Release. 120(3):211-219 (2007).Pubmed
- Trends
in the Exploration of Therapeutic Targets for the Treatment of Endocrine,
Metabolic and Immune Disorders.
X. Chen, C.J. Zheng, L.Y. Han, B. Xie and Y.Z. Chen.
Endocr Metab Immune Disord Drug Targets 7(3):225-231
(2007).Pubmed
- Prediction
of Functional Class of Proteins and Peptides Irrespective of Sequence
Homology by Support Vector Machines.
Z.Q. Tang, H.H. Lin, H.L. Zhang, L.Y. Han, X. Chen, Y.Z. Chen. Bioinformatics
Biol. Insights 1:19-47 (2007).
- Derivation
of Stable Microarray Cancer-differentiating Signatures by a Feature-selection
Method Incorporating Consensus Scoring of Multiple Random Sampling
and Gene-Ranking Consistency Evaluation. Z.Q.
Tang, L.Y. Han, H.H. Lin, J. Cui, J. Jia, B.C. Low, B.W. Li, Y.Z.
Chen. Cancer
Res. 67(20):9996-10003 (2007).Pubmed
- Regression
Methods for Developing QSAR and QSPR Models to Predict Compounds of
Specific Pharmacodynamic, Pharmacokinetic and Toxicological Properties.
C. W. Yap, H. Li, Z. L. Ji and Y. Z. Chen. Mini.
Rev. Med. Chem. 7(11):1097-1107 (2007).
Pubmed
- Prediction of
Factor Xa Inhibitors by Machine Learning Methods. H.H
Lin, L.Y. Han, C.W. Yap, Y. Xue, X.H. Liu, F. Zhu, and Y.Z Chen.
J.
Mol. Graph. Mod. 26(2):505-518 (2007)
Pubmed
- AAIR: Antibody
Antigen Information Resource. Z.Q.Tang,
L.Y. Han, B. Xie, C.Y. Ung, L. Jiang, Z.W. Cao, and Y.Z Chen.
J
Immunol 178(8): 4705 (2007).Pubmed
- Support vector
machines approach for predicting druggable proteins: recent progress
in its exploration and investigation of its usefulness. L.Y.
Han, C.J. Zheng, B. Xie, J. Jia, X.H. Ma, F. Zhu, H.H. Lin, X. Chen,
and Y.Z. Chen.
Drug Discov. Today 12(7-8): 304-313 ( 2007).Pubmed
- Advances in exploration
of machine learning methods for predicting functional class and interaction
profiles of proteins and peptides irrespective of sequence homology
J. Cui, L.Y. Han, H.H. Lin, Z.Q. Tang, Z.L. Ji, Z.W. Cao, Y.X. Li,
and Y.Z. Chen.
Curr. Bioinformatics 2(2): 95-112 (2007).
- Machine Learning
Approaches for Predicting Compounds That Interact with Therapeutic
and ADMET Related Proteins.
H. Li, C.W. Yap, C.Y. Ung, Y. Xue, Z.R. Li, L.Y. Han, H.H. Lin and
Y.Z. Chen.
J. Pharm. Sci.
96(11):2838-2860 (2007).Pubmed
- Are Herb-Pairs
of Traditional Chinese Medicine Distinguishable from Others? Pattern
Analysis and Artificial Intelligence Classification Study of Traditionally-Defined
Herbal Properties.
C.Y. Ung, H. Li, Z.W. Cao, Y.X. Li and Y.Z. Chen.
J. Ethnopharmacol. 111(2):371-377 (2007).Pubmed
- MODEL -- Molecular
Descriptor Lab: A Web-Based Server for Computing Structural and Physicochemical
Features of Compounds. Z.R. Li, L. Y. Han, Y.
Xue, C. W. Yap, H. Li, L. Jiang, and Y. Z. Chen. Biotechnol.
Bioeng 97(2):389-96 (2007).Pubmed
- Computer Prediction
of Cardiovascular and Hematological Agents by Statistical Learning
Methods X. Chen, H. Li, C.W. Yap, C.Y. Ung,
L. Jiang, Z.W. Cao, Y.X. Li and Y.Z. Chen
Cardiovasc. Hematol. Agents Med. Chem.
5(1):11-19 ( 2007).Pubmed
- In Silico
Prediction of Pregnane X Receptor Activators by Machine Learning Approaches.
C.Y. Ung, H. Li, C.W. Yap and Y.Z. Chen. Mol.
Pharmacol. 71(1):158-168 (2007).Pubmed
- PharmGED: Pharmacogenetic
Effect Database B. Xie, C.J. Zheng, L. Y. Han,
S. Ong, J. Cui, H.L. Zhang, L. Jiang, X. Chen and Y. Z. Chen.
Clin. Pharmacol. Ther. 81(1): 29 (2007).Pubmed
- Prediction of
MHC-Binding Peptides of Flexible Lengths from Sequence-Derived Structural
and Physicochemical Properties J. Cui, L.Y.
Han, H.H. Lin, H.L. Zhang, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z.
Chen . Mol. Immunol.
44: 866-877 (2007).Pubmed
- Computer Prediction
of Allergen Proteins from Sequence-Derived Protein Structural and
Physicochemical Properties J. Cui, L.Y. Han,
H.H. Lin, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z. Chen .
Mol. Immunol. 44(4): 514-520 (2007).Pubmed
- PharmGED: Pharmacogenetic
Effect Database. C.J.Zheng,
L.Y.Han, B.Xie, C.Y.Liew, S.Ong, J.Cui, H.L.Zhang, Z.Q.Tang, S.H.Gan,
L.Jiang and Y.Z. Chen.
Nucleic
Acids Res. 35:D794-D799 Sp. Iss. SI (2007)>.Pubmed
- Database of traditional
Chinese medicine and its application to studies of mechanism and to
prescription validation. X Chen, H Zhou, YB
Liu, JF Wang, H Li, CY Ung, LY Han, ZW, Cao and YZ Chen Br.
J. Pharmacol. 149(8):1092-1103 (2006).Pubmed
- Prediction of
the Functional Class of Metal-Binding Proteins from Sequence Derived
Physicochemical Properties by Support Vector Machine Approach. H.H.
Lin, L.Y. Han, H.L. Zhang, C.J. Zheng, B. Xie, and Y.Z. Chen.
BMC
Bioinformatics 7(Suppl 5): S13 (2006).Pubmed
- Classification
of a Diverse Set of Tetrahymena Pyriformis Toxicity Chemical Compounds
from Molecular Descriptors by Statistical Learning Methods
Y. Xue, H. Li, C.Y. Ung, C.W. Yap and Y.Z. Chen
Chem. Res. Toxicol. 19 (8): 1030-1039
(2006). Pubmed
- Usefulness of
Traditionally-Defined Herbal Properties for Distinguishing Prescriptions
of Traditional Chinese Medicine from Non-Prescription Recipes C.Y.
Ung, H. Li, C.Y. Kong, J.F. Wang and Y.Z. Chen.
J. Ethnopharmacol. 109 (1): 21-28 (2006).
Pubmed
- Tannic acid,
a potent inhibitor of epidermal growth factor receptor tyrosine kinase
Bin Yang E, Wei L, Zhang K, Chen YZ, Chen WN .
J Biochem (Tokyo) 139(3):495-502
(2006). Pubmed
- Military vehicle
classification via acoustic and seismic signals using statistical
learning methods Xiao HG, Cai CZ, Chen YZ.
Inter. J. Mod. Phys. C 17 (2):
197-212 FEB (2006).
- PROFEAT: A Web
Server for Computing Structural and Physicochemical Features of Proteins
and Peptides from Amino Acid Sequence. Z.R.
Li, H.H. Lin, L.Y. Han, L. Jiang, X. Chen, and Y.Z. Chen.
Nucleic
Acids Res.Jul 1;34(Web Server issue):W32-7 (2006).Pubmed
- Recent progresses
in the application of machine learning approach for predicting protein
functional class independent of sequence similarity. L.Y.
Han, J. Cui, H.H. Lin, Z.L. Ji, Z.W. Cao, Y.S. Li, and Y.Z. Chen
Proteomics.
Vol.6:
4023-4037 (2006).Pubmed
- MHC-BPS: MHC-Binder
Prediction Server for Identifying Peptides of Flexible Lengths from
Sequence-Derived Physicochemical Properties. J.
Cui, L.Y. Han, H.H. Lin, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z.
Chen Immunogenetics
58(8):607-13 (2006) .
Pubmed
- Application of
Support Vector Machines to in silico Prediction of Cytochrome
P450 Enzyme Substrates and Inhibitors. C. W.
Yap, Y. Xue, Z. R. Li, and Y. Z. Chen Curr.
Top. Med. Chem. 6(15):1593-1607 (2006).Pubmed
- Prediction
of Estrogen Receptor Agonists and Characterization of Associated Molecular
Descriptors by Statistical Learning Methods.
H. Li, C. Y. Ung, C. W. Yap, Y. Xue, Z. R. Li
and Y. Z. Chen. J.
Mol. Graph. Mod. 25 (3): 313-323
(2006).Pubmed
- In silico Search
of Putative Adverse Drug Reaction Related Proteins as a Potential
Tool for Facilitating Drug Adverse Effect Prediction. Z.
L. Ji, Y. Wang, L. Yu, L. Y. Han, C. J. Zheng, and Y. Z. Chen.
Toxicol
Lett. 164:104-112
(2006).
Pubmed
- Information of
ADME-associated proteins and potential application for pharmacogenetic
prediction of drug responses.C.J. Zheng, L.Y.
Han, X. Chen, Z.W. Cao, J. Cui, H.H. Lin, H.L. Zhang, H. Li and Y.
Z. Chen. Curr.
Pharmacogenomics. 4(2):87-103 (2006).
- Therapeutic Targets:
Progress of Their Exploration and Investigation of Their Characteristics.
C.J. Zheng, L.Y. Han, C. W. Yap, Z. L. Ji, Z. W. Cao and Y. Z. Chen.
Pharmacol.
Rev. 58:259-279(2006)Pubmed.
- Increasing the
Odds of Drug Hit Identification by Screening Against Receptor Homologs?
Z.L. Ji, Z.R. Li, J.F. Wang, C.Z. Cai, L.Y.
Han, C.J. Zheng, and Y.Z. Chen. Lett.
Drug. Des. Discov.
3(3):200-204 (2006)
- Progress and
Difficulties in the Exploration of Therapeutic Targets C.J.
Zheng, L.Y. Han, C. W. Yap, B. Xie, and Y. Z. Chen Drug
Discov. Today 11(9-10):412-420 (2006)Pubmed
- Prediction
of Compounds with Specific Pharmacodynamic, Pharmacokinetic or Toxicological
Property by Statistical Learning Methods.
C. W. Yap, Y. Xue, H. Li, Z. R. Li, C. Y. Ung, L. Y. Han, C. J. Zheng,
Z. W. Cao and Y. Z. Chen. Mini.
Rev. Med. Chem. 6:449-459 (2006)Pubmed
- Prediction of
the Functional Class of Lipid-Binding Proteins from Sequence Derived
Properties Irrespective of Sequence Similarity. H.H.
Lin, L.Y. Han, H.L. Zhang, C.J. Zheng, B. Xie, and Y.Z. Chen. J.
Lipid Res. 47(4):824-31 (2006)Pubmed
- PEARLS: Program
for Energetic Analysis of Receptor-Ligand System. L.Y.
Han, H.H. Lin, Z. R. Li, C.J. Zheng, Z.W. Cao, B. Xie, and Y. Z. Chen.
J. Chem.
Inf. Model. 23(1):445-450 (2006)Pubmed
- Traditional
Chinese Medicine Information Database. Z. L.
Ji, H. Zhou, J. F. Wang, L. Y. Han, C. J. Zheng, and Y. Z. Chen.
J.
Ethnopharmacol. 103(3):501 (2006).Pubmed
- Statistical learning
approach for predicting specific pharmacodynamic, pharmacokinetic
or toxicological properties of pharmaceutical agents. H.
Li, C. W. Yap, Y. Xue, Z. R. Li, C. Y. Ung, L. Y. Han, and Y. Z. Chen
Drug Dev. Res. 66:245-259(2006)
- Prediction of
Transporter Family by Support Vector Machine Approach H.
H. Lin, L.Y. Han, C.Z. Cai, Z. L. Ji, and Y.Z. Chen. Proteins.
62
(1): 218-31 (2006)Pubmed
- Quantitative
structure-pharmacokinetic relationships for drug clearance by using
statistical learning methods.
C. W. Yap, Z. R. Li, and Y. Z. Chen.
J. Mol. Graph. Mod 24 (5): 383-395 (2006).Pubmed
- Prediction of
Putative Adverse Drug Reaction-Related Proteins from Primary Sequence
by Support Vector Machines. Z. L. Ji, L. Y.
Han, C. J. Zheng,Z.W. Cao and Y. Z. Chen.
Int. J. of Pharm. Med. 19(5-6):317-322
(2005) .
- Prediction
of Functional Class of Novel Bacterial Proteins without the Use of
Sequence Similarity by a Statistical Learning Method.J.
Cui, L. Y. Han, C. Z. Cai, C.J.Zheng, Z. L. Ji, and Y. Z. Chen.J.
Mol. Microbiol. Biotech. 9 (2): 86-100 (2005)
- Prediction of
Functional Class of the SARS Coronavirus Proteins by a Statistical
Learning Method.C.Z. Cai, L.Y. Han,X.Chen,Z.W.
Cao,Y.Z. Chen. J.
Proteome Res. 4 (5): 1855-1862 (2005).
- Effect of Selection
of Molecular Descriptors on the Prediction of Blood-Brain Barrier
Penetrating and Non-penetrating Agents by Statistical Learning Methods.
H. Li, C. W. Yap, C. Y. Ung,Y. Xue, Z. W. Cao, and Y. Z. Chen.
J.
Chem. Inf. Model. 45 (5): 1376-1384
(2005).
- Prediction of
Functional Class of Novel Plant Proteins by a Statistical Learning
Method. L. Y. Han, C. J. Zheng, H. H. Lin, J.
Cui, H. Li, H. L. Zhang, Z. Q. Tang, and Y. Z. Chen, New
Phytologist. 168:109-121(2005)
- Assessment of
approximate string matching in a biomedical text retrieval problem
. J.F.
Wang, Z.R.Li,C.Z.Cai, and Y. Z. Chen.Comput.
Biol. Med.
35(8): 717-724 (2005).
- TCM-ID: Traditional
Chinese Medicine information database. J. F.
Wang, H. Zhou, L. Y. Han, Z.W. Cao , X. Chen and Y. Z. Chen,Clin.
Pharmacol. Ther.. 78(1):92-93 (2005).
- Prediction of
Cytochrome P450 3A4, 2D6, 2C9 Inhibitors and Substrates by Using Support
Vector Machines. C.W. Yap, Y.Z.Chen
J.
Chem. Inf. Model. 45(4): 982-992 (2005).
- Prediction of
Genotoxicity of Chemical Compounds by Statistical Learning Methods.
H. Li, C. Y. Ung, C. W. Yap, Y. Xue, Z. R. Li, Z. W. Cao, and Y. Z.
Chen. Chem
Res Toxicol.18(6):1071-1080
(2005).
- A Computer Method
for Validating Traditional Chinese Medicine Herbal Prescriptions.
J. F. Wang,C. Z. Cai, C. Y. Kong, Z. W. Cao
and Y. Z. Chen. Am.
J. Chin. Med.33(2):281-297(2005).
- Trends in Exploration
of Therapeutic Targets C.J. Zheng, L.Y. Han,
C. W. Yap, B. Xie, and Y. Z. Chen, Drug
News Perpect. 18(2):109-127 (2005)
- Computer prediction
of drug resistance mutations in proteins. Z.
W. Cao, L. Y. Han, C. J. Zheng, Z. L. Ji, X. Chen, H. H. Lin and Y.
Z. Chen Drug
Discov. Today 10(7):521-529 (2005)
- Effect of training
datasets on support vector machine prediction of protein-protein interactions
S.L. Lo, C. Z. Cai, Y.Z. Chen and Maxey C. M.
Chung.Proteomics.
5(4):876-884 (2005).
- Prediction of
Functional Class of Novel Viral Proteins by a Statistical Learning
Method Irrespective of Sequence Similarity. L.Y.Han,
C.Z Cai, Z. L. Ji, Y.Z. Chen. Virology
331(1):136-143 (2005).
- Quantitative
structure-pharmacokinetic relationships for drug distribution properties
by using general regression neural network. C.
W. Yap, Y.Z.Chen J
Pharm Sci 94(1):153-168 (2005).
- Predicting Functional
Family of Novel Enzymes Irrespective of Sequence Similarity: A Statistical
Learning Approach. L.Y.Han, C.Z.Cai, Z.L.Ji,
Z.W.Cao,J.Cui, Y.Z.Chen Nucleic
Acids Res.32(21): 6437-6444(2004).
- Drug ADME-Associated
Protein Database as a Resource for Facilitating Pharmacogenomics Research.
C.J. Zheng, L. Z. Sun, L. Y. Han, Z. L. Ji, X. Chen, and Y. Z. Chen.
Drug.
Dev. Res.
62:134–142 (2004).
- Density Functional
Theory Studies on Structure, Spectra, and Electronic Properties of
3,7-Dinitrodibenzobromolium Cation and Chloride.X.
H., Y. P. Feng,Y. Z. Chen.J.
Phys. Chem. A, 108:7596-7602 (2004).
- TRMP: A Database
of Therapeutically Relevant Multiple-Pathways. C.J.Zheng,
H. Zhou, B. Xie, L.Y. Han, C.W. Yap, and Y. Z. Chen, Bioinformatics.
20(14):2236-41(2004)
- Effect of molecular
descriptor feature selection in support vector machine classification
of pharmacokinetic and toxicological properties of chemical agents.Xue,
Y.; Li, Z. R.; Yap, C. W.; Sun, L. Z.; Chen, X.; Chen, Y. Z.
J.Chem.
Inf. Comput. Sci. 44,1630-1638(2004)
- Prediction of
p-glycoprotein substrates by support vector machine approach.Xue,
Y.; Yap, C. W.; Sun, L. Z.; Cao, Z. W.; Wang, J. F.; Chen, Y. Z.
J.Chem.
Inf. Comput. Sci. 44(4), 1497-505 (2004)
- MoViES: Molecular
Vibrations Evaluation Server for Analysis of Fluctuational Dynamics
of Proteins and Nucleic Acids. Z.W. Cao, Y.
Xue, L.Y. Han, B. Xie, H. Zhou, C.J. Zheng, H.H. Lin and Y. Z. Chen,
Nucleic Acids Res.32(Web
Server Issue),W679-W685. (2004).
- Prediction of
torsade-causing potential of drugs by support vector machine approach.Yap,
C. W., Cai, C. Z., Xue, Y., and Chen, Y. Z. Toxicol.
Sci. 79(1),170-177. (2004).
- Enzyme Family
Classification by Support Vector Machines.C.Z.
Cai, L.Y. Han, Z.L. Ji, Y.Z. Chen .Proteins.
55,66-76 (2004).
- Prediction of
RNA-Binding Proteins from Primary Sequence by Support Vector Machine
Approach.L.Y. Han, C.Z. Cai, S. L. Lo, Maxey
C. M. Chung,Y. Z. Chen.
RNA. 10(3),355-368. (2004).
- Advances in modeling
of biomolecular interactions.C.Z.Cai, Z.R. Li,
W. L. Wang, Y.Z. Chen. Acta
Pharmacol. Sin.25,1-8(2004).
- Support Vector
Machine Classification of Physical and Biological Datasets.C.Z.
Cai, W.L.Wang, and Y.Z.Chen. Inter.J.Mod.Phys.C
14(5),575 - 585. (2003).
- Protein function
classification via support vector machine approach.C.Z.
Cai ,W.L. Wang, L.Z. Sun, Y.Z. Chen. Math
Biosci, 185, 111-122 (2003).
- Can an In-Silico
Drug-Target Search Method be Used to Probe Potential Mechanisms of
Medicinal Plant Ingredients? X. Chen, C. Y.
Ung, and Y. Z. Chen. Nat.
Prod. Rep., 20, 432 - 444 (2003).
- DART: Drug Adverse
Reaction Target Database. Z.
L. Ji, L. Y. Han, Chun Wei Yap, Li Zhi Sun, Xin Chen, and Yu Zong
Chen .Drug
Safety 26(10),
685-690 (2003).
- SVM-Prot:
Web-Based Support Vector Machine Software for Functional Classification
of a Protein from Its Primary Sequence.C.Z.
Cai, L.Y. Han, Z.L. Ji, X. Chen, Y.Z. Chen. Nucleic
Acids Res., 31(13),3692-3697. (2003).
- Calculation of
Free Energy of the Integrable Landau-Lifshitz Model. C.Z.
Cai, W.L. Wang, Y.Z. Chen.
Chin. Phys. Lett.,
20(7),1009-1012(2003).
- Internet
Resources for Proteins Associated with Drug Therapeutic Effects, Adverse
Reactions, and ADME. Z.
L. Ji, L. Z. Sun, X. Chen, C. J. Zheng, L. X. Yao, L. Y. Han, Z.W.
Cao, J. F. Wang, W. K. Yeo, C.Z. Cai, and Y. Z. Chen.Drug
Discov. Today,
8(12),526-529. (2003).
- KDBI:Kinetic
Data of Bio-molecular Interactions Database. Z.
L. Ji, X. Chen, C. J. Zheng, L.X. Yao, L. Y. Han , W. K. Yeo, P. C.
Chung, H. S. Puy, Y. T. Tay, A. Muhammad, and Y. Z. Chen.
Nucleic.
Acids. Res.,
31(1), 255-257. (2003).
- Correlation between
Normal Modes in The 20-200cm-1 Frequency Range and Localized Torsion
Motions Related to Certain Collective Motions in Proteins. Z.
W. Cao, X. Chen and Y. Z. Chen.J.
Mol. Graph. Mod. 21,309-319.
(2003).
- ADME-AP:
A database of ADME associated proteins.L. Z.
Sun, Z. L. Ji, X. Chen, J. F. Wang, and Y. Z. Chen. Bioinformatics.,
18,1699-1700
. (2002).
- CLiBE: A Database
of Computed Ligand Binding Energy for Ligand-Receptor Complexes and
Its Potential Use in the Analysis of Drug Binding Competitiveness.
X. Chen, Z. L. Ji, D.G. Zhi, and Y. Z. Chen,
Comput.
Biol. Chem. 26, 661-666. (2002).
- Computational
Method for Drug Target Search and Application in Drug Discovery. Y.
Z. Chen, Z. R. Li and C. Y. Ung, J.
Theor. Comp. Chem., 1,
213-224. (2002).
- Absorption,
distribution, metabolism, and excretion-associated protein database
. L. Z. Sun, Z. L. Ji, X. Chen, J. F. Wang,
and Y. Z. Chen,,
Clin.
Pharmacol. Ther. , 71, 405 (2002).
- Computer Automated
Prediction of Putative Therapeutic and Toxicity Protein Targets of
Bioactive Compounds from Chinese Medicinal Plants. Y.
Z. Chen and C. Y. Ung,
Am.
J. Chin. Med.,
30, 139-154. (2002).
- TTD: Therapeutic
Target Database. X. Chen, Z.L. Ji, and Y. Z.
Chen,
Nucleic.
Acids. Res.,
30, 412-415 (2002).
- Inhibition of
epidermal growth factor receptor (EGFR) tyrosine kinase by chalcone
derivatives. E. B. Yang, Y. J. Guo, K Zhang,
Y.Z. Chen, and P. Mack, BBA:
Prot. Struct. Mol. Enzym. 1550,
144-152 (2001).
- Prediction of
Potential Toxicity and Side Effect Protein Targets of a Small Molecule
by a Ligand-Protein Inverse Docking Approach.Y.
Z. Chen, C. Y. Ung, J.
Mol. Graph. Mod., 20, 199-218 (2001).
- Can an optimization/scoring
procedure in ligand-protein docking be employed to probe drug-resistant
mutations in proteins? Y. Z. Chen, X. L. Gu,
and Z. W. Cao, J.
Mol. Graph. Mod. 19, 560-570 (2001).
- A computer approach
for finding putative protein targets of a small molecule. Y.
Z. Chen, FASEB
J 15, A915 (2001).
- Application
of computer-aided drug target search in probing molecular mechanism
of bioactive Chinese natural products. Y. Z.
Chen, and C. Y. Ung, Chin. J. Med.
Chem. 11, 145-148 (2001).
- Ligand-Protein
Inverse Docking and Its Potential Use in Computer Search of Putative
Protein Targets of a Small Molecule. Y. Z. Chen
and D. G. Zhi, Proteins,
43, 217-226 (2001).
- Hydrogen bond
disruption probability in proteins by a modified selfconsistent harmonic
approach. Z. W. Cao and Y. Z. Chen, Biopolymers,
58, 319-328 (2001).
- Computer search
of putative protein targets of a small molecule. Y.Z.
Chen, Biophys.
J. 80, 497A (2001).
- Spontaneous
base flipping in DNA and its possible role in methyltransferase binding.Y.Z.
Chen, V. Mohan, and R. H. Griffey, Phys.
Rev. E62, 1133-1137 (2000).
- Base Opening
in RNA and DNA duplexes: Implication for RNA stability.Y.Z.
Chen, V. Mohan, and R. H. Griffey, Phys.
Rev. E61, 5640-5645 (2000).
- Modified self-consistent
harmonic approach to thermal fluctuational disruption of disulfide
bonds in proteins. Y.Z. Chen, Phys.
Rev. E60, 5938-5942 (1999).
- Molecular basis
for the stereospecificity of Candida rugosa Lipase (CRL) towards ibuprofen.
B. S. Lakshmi, P. Kangueane, Y. Guo., Y. Z.
Chen, and P. Gautam., Biocatal Biotransfor
17, 475-486 (1999).
- Principal Torsion
Angles of Collective Motions in Biomolecules: A Study on Single Base
Opening in DNA Duplexes. Y.Z. Chen, V. Mohan,
and R.H. Griffey, Phys. Rev. E58,
909-913 (1998).
- Effect of backbone
zeta torsion angle on low energy single base opening in B-DNA crystal
structures. Y.Z. Chen, V. Mohan, and R.H. Griffey,
Chem. Phys. Lett. 287, 570 (1998).
- Drug binding
to DNA: Observation of the drug-DNA hydrogen-bond-stretching modes
of netropsin bound to DNA via Raman spectroscopy. S.A.
Lee, A. Rupprecht, and Y.Z. Chen, Phys.
Rev. Lett. 80, 2241 (1998).
- The opening
of a single base without perturbations of neighboring nucleotides:
A study on crystal B-DNA duplex d(CGCGAATTCGCG)2. Y.Z.
Chen, V. Mohan, and R.H. Griffey, J.
Biomol. Struct. Dyn. 15, 765 (1998).
- Recent results
on the statistical mechanis of intergrable models in 1+1 dimensions.
Y.Z Chen, R. K. Bullough, D. J. Pilling and
J. Timonon. World aquaculture.
(1998)
- Theory of DNA
melting based on the Peyrard-Bishop model. Y.L.
Zhang, W.M. Zheng, J.X. Liu, Y.Z. Chen, Phys.
Rev. E56, 7100-7115 (1997).
- A general random
walk model of ATP-driven helicase translocation along DNA. Y.Z.
Chen, Dong Mi, He-Shang Song, and Xian-Ju Wang, Phys.
Rev. E56, 919 (1997).
- Effect of drug
binding induced deformation on the vibrational spectrum of a daunomycin-DNA
complex. Y. Z. Chen, J.W. Powell, S.A. Lee and
E.W. Prohofsky, Phys. Rev. E55,
7414 (1997).
- Calculation
of the binding affinity of the anticancer drug daunomycin to DNA by
a statistical mechanics approach. Y.Z. Chen,
and Yong-Li Zhang, Phys. Rev. E55,
7390 (1997).
- Binding stability
of a cross-linked drug: Calculation of an anticancer drug cisplatin-DNA
complex. Y.Z. Chen, E.W. Prohofsky, and Yong-Li
Zhang, Phys. Rev. E55,
5843 (1997).
- Vibrational
Analysis of Phosphrothioate DNA: II. The POS group in the model compound
dimethyl phosphorothioate [CH_3O)_2(POS)]-. C.A.
Steinke, K.K. Reeves, J.W. Powell, S.A. Lee, Y.Z. Chen, T. Wyrzykiewicz,
R.H. Griffey, and V. Mohan. J.
Biomol. Struct. Dyn. 14, 509 (1997).
- Vibrational
normal modes and dynamical stability of DNA triplex Poly(dA)-2Poly(dT):
S-type structure is more stable and in better agreement with observations
in solution. Y.Z. Chen, J.W. Powell, and E.W.
Prohofsky. Biophys.
J.72, 1327 (1997).
- Sequence dependent
DNA melting predicted by a microscopic statistical theory. Y.
Z. Chen and E.W. Prohofsky, Eur.
Biophys. J. 25, 9 (1996).
- Melting profile
and temperature dependent binding constant of an anticancer drug daunomycin-DNA
complex. Y.Z. Chen and E.W. Prohofsky, Eur.
Biophys. J. 24, 203 (1996).
- Stability and
conformation of [d(T)-d(A)-d(T)](n). Y.Z. Chen
and E.W. Prohofsky, Biophys.
J. 70, SUPM7 (1996).
- Calculation
of the dynamics of drug binding in a netropsin-DNA complex. Y.
Z. Chen and E.W. Prohofsky, Phys.
Rev. E51, 5048 (1995).
- Normal mode
calculation of a netropsin-DNA complex: Effect of structural deformation
on vibrational spectrum. Y. Z. Chen and E.W.
Prohofsky, Biopolymers
35, 657 (1995).
- Sequence and
temperature dependence of the interbase hydrogen bond breathing modes
in B-DNA polymers. Comparison with low frequency Raman peaks and their
role in helix melting. Y. Z. Chen and E.W. Prohofsky,
Biopolymers35,
573 (1995).
- Nonlinear effects
and thermal expansion as expressed in selfconsistent phonon calculations
on the temperature dependence of a phase change: Application to the
B to Z conformation change in DNA. Y.Z. Chen
and E.W. Prohofsky, Phys. Rev. E49,
3444 (1994).
- Premelting base
pair opening probability and drug binding constant of a daunomycin--Poly
d(GCAT)-Poly d(ATGC) complex. Y.Z. Chen and
E.W. Prohofsky, Biophys.
J. 66,
820 (1994).
- Near-neighbor
effects in cooperative modified selfconsistent phonon approximation
melting in DNA. Y.Z. Chen and E.W. Prohofsky,
Phys. Rev. E 49, 873
(1994).
- First or second
order transition in the melting of repeat sequence DNA. Y.Z.
Chen and E.W. Prohofsky,Biophys.
J.66, 202 (1994).
- The role of
thermal flucatuational base pair disruption in DNA-B to DNA-Z conformation
change. Y.Z. Chen and E.W. Prohofsky,Biophys.
J.66, A291 (1994).
- Theoretical
study of the effect of salt and the role of strained hydrogen bonds
on the thermal stability of DNA polymers. Y.Z.
Chen & E.W. Prohofsky, Phys.
Rev. E48, 3099 (1993).
- Salt dependent
premelting base pair opening probabilities of B and Z DNA Poly[d(G-C)]
and significance for the B-Z transition. Y.Z.
Chen & E.W. Prohofsky, Biophys.
J.
64, 1394 (1993).
- Synergistic
effects in the melting of DNA hydration shell: Melting of the minor
groove hydration spine in Poly(dA)-Poly(dT) and its effect on base
pair stability. Y.Z. Chen & E.W. Prohofsky,Biophys.
J. 64, 1385 (1993).
- Differences
in melting behavior between homopolymers and copolymers of DNA: Role
of non-bonded forces for GC and the role of the hydration spine and
premelting transition for AT. Y.Z. Chen &
E.W. Prohofsky, Biopolymers33,
797 (1993).
- A cooperative
self-consistent microscopic theory of thermally induced melting of
a repeat sequence DNA polymer. Y.Z. Chen &
E.W. Prohofsky, Biopolymers33,
351 (1993).
- Theory of presure-dependent
melting of the DNA double helix: Role of strained hydrogen bonds.
Y.Z. Chen & E.W. Prohofsky, Phys.
Rev. E47,
2100 (1993).
- Strained hydrogen-bonds
between Poly(dA).Poly(dT) and its hydration spin and its role in base
pair stability. Y.Z. Chen and E.W. Prohofsky,Biophys.
J.64, A356 (1993).
- Description
of base motion and role of excitations in the melting of Poly(dG)-Poly(dC).
W. Zhuang, Y.Z. Chen & E.W. Prohofsky, J.
Biomol. Struc. Dyn. 10,
403 (1992).
- Energy flow
considerations and thermal fluctuational opening of DNA base pairs
at a replicating fork: Unwinding consistent with observed replication
rates. Y.Z. Chen, W. Zhuang & E.W. Prohofsky,
J.
Biomol. Struct. Dynam. 10,
415 (1992).
- Salt-dependent
stability of Poly(dG)-Poly(dC) with potential of mean force Coulomb
interactions. Y.Z. Chen, W. Zhuang & E.W.
Prohofsky, Biopolymers32,
1123 (1992).
- The role of
a minor groove spine of hydration in stabilizing Poly(dA)-Poly(dT)
against fluctuational interbase H-bond disruption in the premelting
temperature regime. Y.Z. Chen & E.W. Prohofsky,Nucleic.
Acids. Res. 20,
415 (1992).
- Premelting thermal
fluctuational interbase hydrogen bond disrupted states of a B DNA
Guanine-Cytosine base pair. Significance for amino and imino proton
exchange. Y.Z. Chen, W. Zhuang & E.W. Prohofsky,
Biopolymers31,
1273 (1991).
- Premelting thermal
fluctuational base pair opening probability of Poly(dA)-Poly(dT) as
predicted by the modified self-consistent phonon theory. Y.Z.
Chen, Y. Feng & E.W. Prohofsky, Biopolymers
31, 139 (1991).
- A selfconsistent
mean-field calculation of a homopolymer DNA strand separation: bond
breaking in a macromolecule. Y.Z. Chen &
E.W. Prohofsky, J.
Chem. Phys.94,
4665 (1991).
- Criterion of
thermal denaturation for modified-self-consistent-phonon-theory mean-field
calculations in DNA polymers. Y.Z. Chen, Y.
Feng & E.W. Prohofsky, Phys.
Rev. B42,
11335 (1990).
Publications
in the Area of Nonlinear Science
- Thermodynamics
of Toda lattice models: application to DNA. R.K.
Bullough, Y.Z. Chen and J.Timonen, Physica
D
68, 83 (1993).
- Order and chaos
in the statistical mechanics of the integrable models in 1+1 dimensions.
R.K. Bullough, Y.Z. Chen and J.Timonen,
in: Proc. Intl Meeting `Aspects of Nonlinear Dynamics and solitons
and Chaos', eds. I. Antonin and F.J. Lambert, Springer-Verlag,
Heidelberg (1991). pp. 25-37.
- Exact results
in the statistical mechanics of integrable models in (1+1) dimensions.
R.K. Bullough, D.J. Pilling, Y.Z. Chen &
J. Timonon, in: Exact results in quantum dynamics, eds. J.
Dittrich et. al., World Scientific,
Singapore (1991).
- Nonlinearity
and disorder in the statistical mechanics of integrable systems. R.K.
Bullough, J. Timonon & Y.Z. Chen, in: Nonlinearity and
disorder, eds. A.R. Bishop et. al., Springer-Verlag,
Berlin (1991).
- Classical thermodynamics
of the Heisenberg chain in a field by generalized Bethe ansatz method.
R.K. Bullough, Y.Z. Chen, J. Timonon, V. Tognetti
& R. Vaia, Phys.
Lett. A145, 154 (1990).
- Quantum and
classical statistical mechanics of the integrable models. R.K.
Bullough, Y.Z. Chen, Y. Cheng, D.J. Pilling & J. Timonon,
in: Nonlinear evolution equations: integrability and spectral methods,
eds. A. Degasperis, A.D. Fordy & M. Lakshmanan. (Manchester Univ.
Press, Manchester 1990).
- Soliton statistical
mechanics -- thermodynamic limits for quantum and classical integrable
models. R.K. Bullough, Y.Z. Chen & J. Timonon,
in: Nonlinear and turbulent processes in physics, eds. V.G. Baryakhtar,
V.M. Chernousenko, N.S. Erokhin & V.E. Zakharov. (World
Scientific, Singapore, 1990). pp.1377-1422.
- Soliton statistical-mechanics
and the thermalization of biological solitons. R.K.
Bullough, D.J. Pilling, Y. Cheng, Y.Z. Chen and J. Timonen, ,
J. Phys. (Paris) 50 (Suppl 3),
41-51 (1989).
- Statistical
mechanics of the NLS models and their avartars. R.K.
Bullough, Y.Z. Chen, S. Olafsson & J. Timonon. in: Integrable
systems and applications, eds. M. Balabane, P. Lochak & C. Sulem.
(Springer-Verlag, Heidelberg,1989).
12-26.
- Soliton statistical
mechanics and thermalization of biological solitons. R.K.
Bullough, D.J. Pilling, Y. Cheng, Y.Z. Chen & J. Timonon,
in: Nonlinear coherent structures in physics, mechanics and biological
systems, ed. J. Puget. (E.S.P.C.I (Paris) les editions de physique,
Les Uhs, France 1989).
- Statistical
mechanics of integrable models J. Timonon, Y.Z.
Chen & R.K. Bullough, Nucl.
Phys. B 5A, 58 (1988).
- Recent results
on the statistical mechanics of integrable models in 1+1 dimensions.
R.K. Bullough, Y.Z. Chen, D.J. Pilling &
J. Timonon, in: Plasma theory and nonlinear and turbulent processes
in physics, eds. V.G. Bar'yakhtar, V.M. Chernousenko, N.S. Erokhin,
A.G. Sitenko & V.E. Zakharov (World
Scientific, Singapore, 1988).
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