Views of Life
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
· WWW Virtual Library of Cell Biology

· $ MIT Biology Hypertextbook

Introduction /  Chapters /  Syllabus /  Practice Problems /  Quizzes /  Search

· * NIGMS Digital Textbooks on Life Sciences
Genes & Populations  /  Genetic Basics /  The Structures of Life /  Findings /  The Chemistry of Health
· $ DOE Primer on Molecular Genetics

· * L. Hunter.  Molecular Biology for Computer Scientists. In Artificial Intelligence and Molecular Biology, L. Hunter editor, 1993, AAAI Press.

· The American Society for Cell Biology
· Cell Biology Education

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 topic
e-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 A: Technology Fundamentals
· Optical Microscope, Nomarski Optics · Electron Microscope
· X-ray crystallography
· SOR (Synchrotron Orbital Radiation) · NMR (Nuclear Magnetic Resonance)
· Mass Spectroscopy(MS)
· AMS (Accelerated MS)

Computational Chemistry    >>Top

Using Computers in Teaching Chemistry
· CAChe
· HyperChem
· Journal of Chemical Education Software
· LabWorks
· LUCID Learning and Understanding through Computer-based Interactive Discovery
· Mathcad
· Mathcad Documents for Physical Chemistry
· Mathematical Modeling of Chemical Phenomena
· Molekel

· Online educational systems · Spartan
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

· 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
  • · GAUSSIAN
  • · GAMESS : The General Atomic and Molecular Electronic Structure System
  • · FMOM : Fragmented Molecular Orbital Method(Japanese)
Molecular Dynamics
· $ AMBER : Force Field Caluculation
· $ CHARMM tutorial CHARMM documentation
· GROMOS
· $ 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)
· PEACH
· $ SCL

Bioinformatics    >>Top

Text Books

  • · Cynthia Gibas and Per Jambeck, Developing Bioinformatics Computer Skills, O”ĒREILY, 2001
  • · D.M.Mount, Bioinformatics, Cold Spring Harbor Laboratory Press,NY,2001

Bioinfomatics Resource Giude

  • · Websites

Where can you study bioinformatics ?

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

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

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

Genome Wide Data Analyses Tools Mapping Molecular Interactions
  • · Cell Signaling Pathways and Networks
    • · AfCS-Nature Signaling Gateway
    • · STKE(Science)
    • · 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 
    • · TRANSFAC
    • · Cell Signaling Network Database(CSNDB)
    • · BioCarta Pathways

Systems Theory and Systems Biology    >>Top

Text Book

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
    • · CERS
  • · 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

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

Science of Cancer

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. 1

Drug Databases 

  • · JAN /Japanese Pharmacopoeia
  • · USAN
  • · INN

Drugness and Drugability Analysis

  • · 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

  • · P450 Database for Drug Interactions
  • · CytochromeP450(CYP)related site
  • · 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

Internal Targets of Xenobiotic Chemicals

QSAR when the targets are unknown

Target 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
    • · Receptor Database
    • · $ Kotoko Nakata, et al,Extension of The Receptor Database (RDB),Chem-Bio Informatics Journal ,Vol. 1 (2001) , No. 3
    • · $ Kotoko Nakata, et al, An Integrated Receptor Database(IRDB),Data Science Journal,Vol. 1,Issue 2,Augast(2002)
  • · Drug Target Database
  • · Focused Library 

Computer-aided Drug Design

Docking study when the targets are known

Virtual Screening ? Computer aided HTS

  • · Rational Drug Design

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
  • · Zacharewski Laboratory: In Silico Toxicology
  • · Dioxin Research Portal

Adverse Effects

Venders for Genomic Drug Design

Genome Based Clinical Medicine    >>Top

Virtual Patients : From Cell Models to Physiological Models 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)
Nuclear Receptor Research Portal
New Topics in Informatics and Computing    >>Top
Grid Computing
Biochemical Prospecting    >>Top

Foods and CAM    >>Top

  • · Designer/Functional Foods 
  • · CAM (Complemetary and Alternative Medicine)
  • · Food Safety
  • · Anti-Aging Physicians Society(AAPS)
Theoretical Approach to Life   >>Top
Books for Physicists who are interested in biology  >>Top
Below is Kaminumafs personal collection of books that are highly recommendable for physicists who are interested in life. These books touch on such important and fundamental topics as how physicists should approach to biology, life as computing machine, life as developing machine, and how life accumulated these kinds of properties through long history of evolution.
  • · John Maddox, What Remains To Be Discovered, Macmillan, London, 1998
  • · Freeman Dyson, The Future of Physics, Physics Today, 1970, also in F. Dyson, From Eros to Gaia, Pantheon Books, NY, 1992, pp.151-159
  • · John von Neumann, The Computer and the Brain, Yale Univ., New Haven, 1958
  • · Manfred Eigen and Ruthild Winkler, Laws of the Game-How Principles of Nature Govern Chance, Princeton Univ. Press, 1993 (translated from German edition, Naturgesetze steuern den Zufall, R. Piper & Co., Verlag, Munich, 1965)
  • · Richard P. Feynman (J.G. Hey and R.W. Allen eds.), Feynman Lecture on Computation, Addison Wesley, 1996
  • · Richard P. Feynman, Therefs Plenty of Room at the Bottom, A Talk to American Physical Society on December 29, 1959 at Caltech, also in Richard P. Feynman (Jeffery Robbins ed.), The Pleasure of Finding Things Out, Perseus Pub., 1999, pp.117-139
  • · Murray Gell-Mann, The Quarks and the Jaguar-Adventures in the Simple and the Complex, Little, Brown and Company, London, 1994 
  • · Stuart Kauffman, AT HOME IN THE UNIVERSE-The Search for the Lawsof 
  • Self-Organization and Complexity, Oxford Univ., 1995
  • · Peter Coveney and Roger Highfield, Frontiers of Complexity-The Search for Order in a Chaotic World, Random House, NY, 1995
  • · Levin Kelly, Out of Control-The New Biology of Machines, Fourth Estate Limited, London, 1994
  • · Roger Penrose, The Emperorfs New Mind-Concerning Computers, Minds, and Laws of Physics, Oxford Univ. Press/Penguin Books, 1989
  • · Roger Penrose, Shadows of the Mind, Oxford Univ. Press, 1994 
  • · John H. Holland, Hidden Order-How Adaptation Builds Complexity, Addison-Wesley, 1995
  • · Ian Stewart, Lifefs Other Secret-The New Mathematics of the Living World, Penguin Books Ltd., London, 1998
  • · Richard Dawkins, The Selfish Gene (new edition), Oxford Univ. Press, NY, 1989 (First edition in 1976)
  • · Richard Dawkins, the extended phenotype-The long reach of the gene, Oxford Univ. Press, 1982
  • · Richard Dawkins, The Blind Watchmaker-Why the evidence of evolution reveals a universe without design, Norton, 1987
  • · Christopher Wills, The Wisdom of the Genes-A New Pathway to Evolution, HarperCollins, 1989
  • · Robert J. Richards, The Meaning of Evolution, University of Chicago Press, 1992
  • · George C. Williams, Natural Selection-Domains, Levels, and Challenges, Oxford Univ. Press, 1992
  • · Stephen Jay Gould, Wonderful Life-The Burgess Shale and the Nature of History, Norton, NY, 1989
  • · Stephen Jay Gould, Lifefs Grandeur-The Spread of Excellence from Plato to Darwin, Random House, 1997
  • · Simon Conway Morris, the Crucible Creation-The Burgess Shale and the Rise of Animals, Oxford Univ. Press, 1998

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