Last Update 22.11.2002
Area of Interests
Views of Life >>Top
Physist View
- Erwin O. Schrodinger, What is Life ?
- Stephen C. Meyer
- Alan Turing, Turing Machine as a Model of Computer
- John von Neuman, Theory of Self-Reproduing Automata, University of Illinois Press, 1966, Complied by Arther W. Burks.
Biology Tutorial >>Top
Introduction / Chapters / Syllabus / Practice Problems / Quizzes / Search
- NIGMS
Genes & Populations / Genetic Basics / The Structures of Life / Findings / The Chemistry of Health
- DOE
- * L. Hunter. Molecular Biology for Computer Scientists. In Artificial Intelligence and Molecular Biology, L. Hunter editor, 1993, AAAI Press.
Books
- B. Alberts et al. , Molecular Biology of the Cell, Garland, 199X?
- Cambridge Health Institute is good source for BioIT in general
(Glossary homepage/Search) is a huge digital encyclopedia on this topice-Learning
Role of Physics in Modern Biology : Physics plays important roles in the DOE/Genome to Life Project >>Top
- Genomes to Life
Measurement of Structure of Living Systems
- $ Genomes to Life : Appendix : Technology Fundamentals
- Optical Microscope, Nomarski Optics
- Electron Microscope
- X-ray crystallography
- SOR (Synchrotron Orbital Radiation)
- Spring-8
- The National Neutron Light Source at Brookhaven National Laboratory
- Advanced Light Source at Lawrence Berkeley National Laboratory
- NMR (Nuclear Magnetic Resonance)
- Mass Spectroscopy(MS)
- AMS (Accelerated MS)
Computational Chemistry >>Top
Using Computers in Teaching Chemistry
- CAChe
- Journal of Chemical Education Software
- LabWorks
- LUCID Learning and Understanding through Computer-based Interactive Discovery
- Mathcad
- Mathcad Documents for Physical Chemistry
- Mathematica
- Mathmatical Modeling of Chemical Phenomena
- Molekel
- Online educational systems
Reference Sites
- WWW Computational Chemistry Resources,
- NLM Chemical Information
- $ NIH Molecular Model Tutorial
- $ Introduction to Macromolecular Simulation
Molecular Representation
- Molecular Registration
- CAS No : Chemical Abstract Service Registry Number
- Molecular Formula and Molecular Drawing
- 3D atomic coordinates and Molecular Graphics
- Molecular Structure and Nomenclature Database
- MDL, ISIS
- $ ChemFinder
- Math Mol : Molecular Modeling
Exercise: How to develop a chemical database ?
Molecular Computation
- What can we compute?
- Structure and Reactivity
- Classical models:Molecular Mechanics
- $ AMBER : Force Field Caluculation
DNA / Plastocyanin,ion,water / NMR refinement of a DNA duplex / Generalized Born solvent model / Simple free energy example / Streptavidin,biotin complex, partially solvated / Crown ether in vacuum / Methane in water box
- Quantum chemistry: Semi-Empirical MO Method
- Quantum chemistry: ab initio MO Method
Molecular Dynamics
- $ CHARMM tutorial : Table of Content
- CHARMM documentation
- $ NAMD : NIH Resource for Macromolecular Modeling and Bioinformatics
- $ Emad Tajkhorshid, et al, Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning, Science 2002 April 19; 296: 525-530. (in Reports)
- $ SCL
Bioinformatics >>Top
Text Books
- Cynthia Gibas and Per Jambeck, Developing Bioinformatics Computer Skills, OREILY, 2001
- Bioinformatics, Cold Spring Harbor Laboratory Press
Bioinfomatics Resource Giude
Where can you study bioinformatics ?
- Universities
- Introduction to Bioinformatics and Genomics : City University of New York
DNA Databases International
- NCBI (National Center for Biotechnology Information)
- EMBL (European Molecular Biology Laboratory)
- DDBJ (DNA Data Bank of Japan)
Protein (Amino Acid) Sequence Database
Sugar and Lipid Molecular Databases
Genome Sequence Data
- $ Human genome Project Imformation Announcements
- $ Nature Genetics Information
- Access to Genome Databases
- $ A User's Guide to the Human Genome
Genetic Variation and Personalized Medicine
- SNPs/Micro Satellites
- Pharmacogenomics and FDA Policy
- $ FDA : Lesko LJ, Woodcock J.,Pharmacogenomic-guided drug development: regulatory perspective.,Pharmacogenomics J 2002;2(1):20-4
3D Structure of Biomolecules
- Protein Structure:
- $ PDB : Protein Data Bank (Research Collaboratory for Structural Bioinformatics RCSB)
- PDB soft ware list
- Structure Genomics-A Post Genome Challenge
Molecular Graphics and Modeling for Biomolecules
Docking Study of Xenobiotic Chemicals and Target Biomolecules
- $ Ruben Abagyan Lab Group
- $ AutoDock : The Scripps Research Institute
- $ Tools for AutoDock
Peptide-Protein Interaction
- $ DOT : San Diego Super Computer Center (SDSC)
Simulation of Protein Folding -A Grand Challenge in Chemical Computing
Modeling Cell World >>Top
Genome Wide Simultaneous Measurements
- DNA chip and Microarray
- Proteomics
- Metabolomics/Metabonomics
- Jeremy K. Nicholson et al., Metabonomics : a platform for studying drug toxicity and gene function, Nature Reviews : Drug Discovery, Vol.1,Feburary153-162(2002)
- Homepage of Chemometrics
- Metabometrix
Genome Wide Data Analyses Tools
Mapping Molecular Interactions
- Biochemical Synthesis and Metabolism Maps
- Cell Signaling Pathways and Networks
Heinemeyer, T. et al., Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanism, Nucleic Acids Res., 27, 318-322 (1999). TRANSFAC Release 4.0 - Documentation
Systems Theory and Systems Biology >>Top
Cell Simulator : Virtual Cell
Frontiers of Bio Sciences >>Top
Comparative Genomics
Developmental Biology-The True Mystery of Life
- Development : The process from zygot to adult
Two big events in life - gastrulation and neurulation- C.elegans the most known multicellular organism
- Developmental genes, proteins, chemicals, and pathways
- Gilbert, Development Biology?
- Scott F. Gilbert, Development Biology 6th edition, Sinauer Associate, 2000
- Lewis Wolpert, Principles of Development 2nd, Oxford Univ. Press, 2002
Endocrine System
- $ Understanding Estrogen Receptors, Tamoxifen, and Raloxifene (National Cancer Institute: Science Behind the News)
Endocrine Disruptor Hypothesis
IPCS, Global Assessment of the State-of-the-Science of Endocrine Disruptors
Chemical Database for Endocrine Disruptors
Neural System and Brain
- Eric R. Kandel, James H. Schwartz, and Thomas M. Jessell, Principles of Neural Science 4th edition, McGraw-Hill, 2000
Immune System
- National Cancer Institute Tutorial: Understanding the Immune System
- * Alan S. Perelson and Gerard Weisbuch, Immunology for physicists, Reviews of Modern Physics, Vol. 69, Nov. 4, October, pp.1219-1267(1997)
Science of Cancer
- Junghans TB, Sevin IF, Ionin B, Seifried H., Cancer information resources: digital and online sources, Toxicology ,Apr 25;173(1-2):13-34( 2002)
NCI Tutorial
Abnormal cell proliferation
Apoptosis – Program cell death
Chemical Carcinogen
Quest for Drugs and Safety Control of Chemicals >>Top
PHII Project
- $ Tsuguchika Kaminuma, et al, Pharmacoinformatics Infrastructure for Genome-based Personalized Medicine,
Chem-Bio Informatics Journal, Vol. 1 (2001) , No. 1Drug Databases
- JAN /Japanese Pharmacopoeia
- USAN
- INN
Drugness and Drugability Analyses
- Isao Fujii, et al, Essential Chemical Characteristics for Drugs,Chem-Bio Informatics Journal,Vol. 1 (2001) , No. 1 18-22
- C.A.Lipinski,F.Lombardo, B.W.Dominy and P.J.Feeney, Adv. Drug Delivery Rev., 23, 3-25 (1997)
Good effects and bad effects are two sides of the same coin.
ADME :
Absorption, Distribution, Metabolism, Excretion
Fate of Drugs and Xenobiotic Chemicals in living organisms
$Lovisa Afzelius, et al, Masimirembwa,Competitive CYP2C9 Inhibitors: Enzyme Inhibition Studies, Protein Homology Modeling, and Three-Dimensional Quantitative Structure-Activity Relationship Analysis, Mol Pharmacol 2001 59: 909-919.
$Sean Ekins, et al, Pharmacophore and Three-Dimensional Quantitative Structure Activity Relationship Methods for Modeling Cytochrome P450 Active Sites, Drug Metab Dispos 2001 29: 936-944.
$Human membrane Transporter DB(AAPS PharmSci)
Toxicity Prediction: e-Tox
- QSAR:
Internal Targets of Xenobiotic Chemicals
QSAR when the targets are unknownTarget hunting – search for disease related genes
- International Human Genome Sequencing Consortium, International sequencing and of the human genome, Nature, Vol.409, 15 February, 2001,(pp.912 Drug Targets)
The Concept of Receptors and Ligands
Receptor Database
$ Kotoko Nakata, et al,Extension of The Receptor Database (RDB),Chem-Bio Informatics Journal ,Vol. 1 (2001) , No. 3
$ otoko Nakata, et al, An Integrated Receptor Database(IRDB),Data Science Journal,Vol. 1,Issue 2,Augast(2002)
- Drug Target Database
- $ Pharmainformatics Databases:University of Singapore
- Focused Library
Computer-aided Drug Design
Docking study when the targets are known
Virtual Screening – Computer aided HTS
Computational Toxicology
- $LCBRA
- Philip Wexler
- National Center For Toxicological Research/Center for Computational Toxicology
- National Institute of Environmental Health Sciences, Endocrine Disruptor DB
- National Institute of Health Sciences : $ Endocrine Disruptor Information for Researchers
- QSAR DB for Endocrine Disruptors
- $ Kazuo Koyano, et al,Electrostatic Potentials and CoMFA Analysis of Toxicity of Dioxins, Chem-Bio Informatics Journal, Vol. 1 (2001) , No. 2
- Zacharewski Laboratory: In Silico Toxicology
Adverse Effects
FDA MedWatch"Fda Safety Information and Adverse Event Reporting Program"
the Uppsala Monitoring Centre (WHO Adverse Reactions Database)
Venders for Genomic Drug Design
Genome Based Clinical Medicine >>Top
Virtual Patients from Cell Models to Physiological Models
- Cancer : Gene Network Sciences (GNS) Inc.
- Cardio Vascular Disease : Physiome Sciences
- Obesity, Diabetes : Entelos
- Large Scale Bioloogy Corp. (LSB)
- Immunological Diseases: ISB (Institute of Systems Biology)
- Beyond Genomics, Inc.
- Gene Network Sciences
NR and Disease Modeling: Kaminuma/CBI
- Nuclear Receptor Support site
- Clinical Guidelines on the Identification, Evaluation, and Treatment of Overweight Obesity in Adults : NIH
Genetic Variation and Personalized Medicine
- SNPs/Micro Satellites
- Kotoko Nakata, et al, An Agent System for Collecting SNPs Data on the Internet, Chem-Bio Informatics Journal ,Vol. 1, No. 3 120-123, (2001)
- Compugen
- Pharmacogenomics and FDA Policy : Lesko, L. J., Woodstock, J., "Pharmacogenomic-guided drug development: regulatory perspective", The Pharmacogenomics Journal 2:20-24 (2002)
New Topics in Informatics and Computing >>Top
Grid Computing
Biochemical Prospecting >>Top
- WHO Policy and Strategy on Traditional Medicine
- J.C. Schuster, Chemical Prospecting: Evoulutionary-Biogeographical Approach-Mesoamerican Cloud Forests as an Example, Pure Appl. Chem., Vol. 70, No. 11, pp. 2112, 1998
- Health Sharman.com
- PhytoPharm
- University of Singapore, Bioinformatics and Drug Design Group
- Qiao X, Hou T, Zhang W, Guo S, Xu X.:A 3D structure database of components from Chinese traditional medicinal herbs,J Chem Inf Comput Sci 2002 May-Jun;42(3):481-9
- NAPRALAET(NAtural PRoducts ALERT):Univ. of Illinois
- MEDFLOR
- Traditional Medicine and Medicinal Plants in Cuba
- Peter Schwab,Cuba confronting The U.S. embargo, St. Martin's Griffin p53-79.(1999)
- CUBA: Natural Medicine Gains Wide Acceptance
- Pan American Health Organization(2001)"Country Report on Cuba"
- With Drugs Scarce, Cuba Tries Natural Cures
- Myths And Facts About The U.S. Embargo On Medicine And Medical Supplies
- Dreaming with Two Feet on the Ground-Acupuncture in Cuba
- The Collapse of the Soviet Union and the Eastern Bloc: Effects on Cuban Health Care
- Mercedes Garcia, Green Medicine : An Option of Richness, Sustainable Agriculture and Resistance, Food First(2002)
- The Big Green Experiment: Cuba's Organic Revolution
- Living on earth, November 4, 1994
- Primary Care in Cuba : Low-and High Technology Developments Pertinent to FamilyMedicine
- Cuba to Develop Synthesis Between Conventional and NaturalMedicine
- 3rd Annual Congress of Natural/Alternative Medicine and Bioenergetics
Foods and CAM >>Top
- Food Safety
- Designer/Functional Foods
- CAM (Complemetary and Alternative Medicine)
- www.Foodsafety.gov.
Theoretical Approach to Life >>Top
- Santa Fe Institute
Stuart Kauffman
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