Welcome to

Who we are? Bioinformatics & Drug Design group [BIDD] is a research group based in Department of Pharmacy, Faculty of Science, National University of Singapore. Our group is active in computer-aided drug design, machine learning, pharmainformatics and cheminformatics, computational biology and bioinformatics, herbal medicine, and art and sciences.What we do? We have been developing computational methods, software tools and databases for drug discovery, target discovery, protein function prediction modeling of biological systems, network descriptor, and biomarker discovery, leading to one US patent, 13 databases, 9 web-based software tools, 3 art and science web-servers, and >230 papers published in such international journals as Nature Reviews Drug Discovery, Natural Biotechnology, PNAS, Natural Product Reports, Cancer Research, Nucleic Acids Research, and Journal of Immunology.Milestones! We pioneered inverse docking method for drug target discovery, developed the popular therapeutic target database, and are among World's first in exploring machine learning methods for protein function prediction, ADME-Tox prediction, target discovery, multi-target virtual screening.Our Alumni! BIDD alumni remain active in academic and research careers as faculty members in TongJi University, XiaMen University, ZheJiang University, Boston University, Mayo Clinic, University of Nebraska, NanJing University, SiChuan University, and National University of Singapore, as senior scientists in NIH, Harvard University, University of Georgia, National University of Singapore, A*Star IMCB and BII, and as PIs in pharmaceutical companies such as Novartis and Merk MSD.

People

Chen Yu Zong, Ph.D.

Tenured Professor
Department of Pharmacy, Faculty of Science
National University of Singapore

Chen Yu Zong is a Tenured Professor in the Department of Pharmacy, Faculty of Science at National University of Singapore and a member of NUS Graduate School for Integrative Sciences and Engineering (NGS). He is the pioneer of 'Inverse Docking' method for drug discovery, the developer of the popular database "Therapeutic Target Database (TTD)", a researcher among World's first in exploring machine learning methods for protein function prediction, ADME-Tox prediction, target discovery, and multi-target virtual screening, the recipient of the Outstanding Scientist Award 2007 (Science Faculty, NUS). His research has led to one US patent, 13 databases, 9 web-based software tools, 3 art and science web-servers, and >230 peer-reviewed publications. Chen Yu Zong received his Ph.D. in Physics from University of Manchester, Institute of Science and Technology, U.K. in 1989. Before coming to NUS, he spent four years as Post-Doc fellow at Biophysics Group, Dept of Phys, Purdue University, Indiana, USA.

Email: Prof. Chen Yu Zong
Research Profile: Google Scholar

Current Team

Dr. Qin Chu

Post Doc
2015.08 - Now
phaqc@nus.edu.sg

Dr. Chen Shangying

Post Doc
2017.05 - Now
phacs@nus.edu.sg

Mr. Zeng Xian

PhD Candidate
2014.08 - Now
zengxian@u.nus.edu
Google Scholar

Mr. He Weidong

PhD Student
2016.01 - Now
weidong@u.nus.edu

Ms. Wang Yali

PhD Student
2016.08 - Now
e0021499@u.nus.edu

Prof. Zhao Hongping

Visiting Scholar
2017.01 - Now

Prof. Wu Jianbing

Visiting Scholar
2017.10 - Now

Databases

Bioinformatics Databases

  • HEROD: Human Ethnic and Regional specific Omics Database

  • CLiBE: Computed Ligand Binding Energy

  • KDBI: Kenitic Data of Biomolecule Interactions
  • Pharmainformatics Databases

  • TTD: Therapeutic Target Database

  • CFam: Chemical Families Database

  • DART: Drug Adverse Reaction Target
  • ADME-Associated Protein
  • Therapeutically Relavent Multiple Pathways
  • Pathway Crosstalk Database
  • Information of Drug Activity Data
  • Server for Pharmacophore Information and Mapping
  • Herbinformatics Databases

  • TCM-ID: Traditional Chinese Medicine Information Database

  • NPASS: Natural Product Activity and Species Source Database
  • Softwares

    A Protein Functional Family Prediction Web-Server

    A Web-Server for Compting Protein Features of Multiple Categories

    A Software for Predicting Targets of Small Molecules

    Arts

    Exhibit Beauty and Knowledge of Science with High-quality Digital Artworks

    Generate Music of Protein Sequences

    Express the Beauty and Science of Pharmaceuticals

    Teaching

  • CZ5225: Modeling and Simulation in Biology
  • CZ5226: Advanced Bioinformatics
  • CZ1103: Introduction to Computational Science
  • CZ2106: Simulations
  • LSM2104: Essential Bioinformatics and Biocomputing
  • LSM3241: Bioinformatics and Biocomputing
  • CZ3253: Computer Aided Drug design
  • CZ3272: Monte Carlo and Molecular Dynamics
  • CZ4101: Matrix Computations
  • CZ4102: High Performance Computing
  • CZ4226: Advanced Bioinformatics
  • CZ4275: Condensed Matter: Simulation and Computation
  • CZ5211: Topics in Computational Biology
  • SMA5422: Special Topics in Biotechnology
  • Computer Aided Drug Design
  • Cross-Department biocomputing lecture and lab sessions
  • SMA5233/CZ5206, Particle Methods and Molecular Dynamics
  • Research

    Research Interests

    Our research interests are in the areas of Machine Learning-aided Drug Design, Computational Biology and Bioinformatics. These are interdisciplinary areas still in development and grow rapidly along with advances in life scince, computational techniques, and computer technology. The objective of our research is to develop innovative software tools and databases to facilitate new drug discovery. We have also been doing basic research in computational biology. Life science is an information intensive science. As a result, computer tools and IT technology are expected to play a key role in the research and development of drugs as well as other fields in biological and medical sciences. This combination of information technology into biotechnology is both challenging and rewarding.

    Selected Publications

    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).PubMed 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).PubMed
    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).PubMed 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).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 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

    Patents

    Opportunities

    PhD Programs, Research Fellowships, Assistantships:

    • Applications are invited for graduate study leading to Ph.D. in bioinformatics, biomodeling, drug-design and biophysics.
    • Full-time research scholarship, which covers tuition and stipend (S$2,000/mo before QE-II exam, S$2,500/mo after QE-II exam), will be offered to each successful candidate. Besides, applicants are also encouraged to apply for NGS Scholarship which covers all tuition, stipend (S$3000/mo for interational students) for 4-years, and computer/book/conference allowance for oversee conferences.
    • Positions for research fellowships and assistantships are also available for those who have already got a M.Sc or Ph.D.

    Specific projects include:

    • Artificial Intelligence-based Drug Design and Discovery
    • Bioinformatics and Pharmainformatics Database Development
    • Mechanism of Chinese Medicinal Plant Drugs
    • Modeling of Protein Motions and Dynamics
    • Prediction of Protein Function and Protein-Protein Interactions
    • Understanding Mechanisms of Complex Diseases Based on Human Health Big Data
    • Simulation of Biological Pathways

    Collaborations


    CONTACT US





    Mailing Address
    Tahir Foundation Building, Level 5
    12 Science Drive 2, Singapore 117549

    Email: Prof. Chen Yu Zong [phacyz@nus.edu.sg]