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DRAFT
Information resources: Combinatorial chemistry, chemogenomics and cheminformatics
Mary Chitty mchitty@healthtech.com
617-630-1316 not being updated
Information resources:
Combinatorial chemistry, Chemical genomics Chemical
genomics definitions & overviews Combinatorial
chemistry definitions & overviews
Information resources: Bibliographies
Databases Journals
News
Websites Terminology
Cheminformatics Information Resources
Terminology Medicinal & pharmaceutical chemistry
Chemistry
Bibliographies
Gary Wiggins, Cheminfo, Indiana
University http://www.indiana.edu/~cheminfo/index.html
Guide to Selected
Biotechnology Resources at Stanford Univ., Swain Chemistry & Chemical
Engineering Library, 2003
http://www-sul.stanford.edu/depts/swain/libguides/biotechnology/table.html
Open Directory Project
OPD Biochemistry http://dmoz.org/Science/Biology/Biochemistry_and_Molecular_Biolo.../
Royal Society of
Chemistry, Guide to Chemistry Resources on the Internet http://www.rsc.org/lic/selectsites.htm
Chemistry
Databases
Chemical Abstracts http://www.cas.org/
Gene sequences are indexed in Chem Abstracts, and assigned registry
numbers.
Combinatorial and
Chemogenomics Journals
BMC
Biochemistry, BioMedCentral, 2000- http://www.biomedcentral.com/bmcbiochem/
All aspects of biochemistry, including metabolic pathways, enzyme functions, and
small molecular components of cells and tissues
Biochimica et
Biophysica Acta: http://www.elsevier.com/wps/find/journaldescription.cws_home/506062/description#description
Biomembranes, Elsevier, 1967-
Main focus is on membrane structure, function and biomolecular organization,
membrane proteins, receptors, channels and anchores, fluidity and composition,
model membranes and liposomes, membrane surface studies and ligand interactions,
transport studies, and membranes dynamics.
Biochimica et
Biophysica Acta: Gene Structure and Expression, Elsevier, 1982-
BBA's Gene Structure and Expression covers DNA and RNA structure, DNA
replication, damage and repair, gene re-arrangements and recombination, control
of gene expression, transcription and translation mechanisms, RNA processing,
cell-cycle control, nucleic acid- ligand interactions, DNA- modifying enzymes,
viral systems and molecular genetics. Also includes Short
functional sequence- papers describing DNA and RNA sequences for protein coding,
regulatory or structural elements combined with significant functional studies,
and Promoter papers describing sequence and functional analysis of promoter and
enhancer regions. Papers on
functional genomics that provide significant experiments that address the
function of genes whose sequences and not function are already established.
Biochimica et
Biophysica Acta: Molecular Basis of Disease, Elsevier,
1990-
Addresses the biochemistry and molecular genetics of disease processes and their
models. The section covers metabolic, membrane, receptor and immunological
disorders as well as viral, bacterial and parasitological diseases, and includes
the biochemistry of differentiation disorders, tissue damage and aging.
Biochimica et
Biophysica Acta Molecular Cell Research, Elsevier,
1982-
This section focuses on cellular processes at the molecular level. These include
aspects of intracellular trafficking, regulation of the secretory and endocytic
pathways, sorting and targetting, organisation and dynamics of cytoskeletal
structures, cellular interactions, cell cycle regulation, cell/tissue
differentiation and cellular enzymology. Also included are studies at the
interface between Cell Biology and Biophysics which apply for example novel
imaging methods for characterizing cellular processes. Excluded, however, are
studies describing purely cellular or pharmacological aspects
Biochimica et
Biophysica Acta Reviews on Cancer, Elsevier, 1974-
Covers the whole field of the biology and biochemistry of cancer, emphasizing
oncogenes and tumor suppressor genes, growth-related cell cycle control
signalling, carcinogenesis mechanisms, cell transformation, immunologic control
mechanisms, genetics of human (mammalian) cancer, control of cell proliferation,
genetic and molecular control of organismic development, rational anti-tumor
drug design. In short, the journal presents critical reviews on new developments
in cancer investigation at the molecular level
BMC Chemical biology, BioMedCentral,
2001- [electronic] http://www.biomedcentral.com/bmcchembiol
Application of chemistry to the investigation of biology and drug design.
ChemBioChem, Wiley,
2000- http://www3.interscience.wiley.com/cgi-bin/jhome/72510898 Mission is to integrate this wide and flourishing field,
ranging from complex carbohydrates through peptides/ proteins to DNA/ RNA, from
combinatorial chemistry and biology to signal transduction, from catalytic
antibodies to protein folding, from bioinformatics and structural biology to
drug design.
Chemico-biological
interactions, Elsevier, 1969- http://www.elsevier.com/locate/chembioint
Molecular, cellular, and/ or biochemical basis of toxicologically relevant
outcomes. Special emphasis is placed on mechanisms associated with interactions
between chemicals and biological systems. Outcomes may include all traditional
endpoints caused by synthetic or naturally occurring chemicals, both in vivo
and in vitro. Endpoints of interest include, but are not limited to,
carcinogenesis, mutagenesis, respiratory toxicology, neurotoxicology,
reproductive and developmental toxicology, and immunotoxicology.
Chemistry and
Biology, Cell Press, 1994- Interface between chemistry and biology, including the
use of natural and designed molecules as probes of cellular pathways; rational
drug design based on knowledge of the structure and/or function of the target
molecule; the nature of molecular recognition in biological systems; novel
procedures for the large- scale analysis of genes and proteins; functional and
structural genomics; proteomics; molecular basis of evolution; chemical insights
into signaling, catalysis, and gene expression; and novel chemical and
biological methods for molecular design, synthesis, and analysis.
Combinatorial
Chemistry and High Throughput Screening,
Bentham 1998- http://www.bentham.org/cchts/index2.html
Small
molecules, peptide, nucleic acid or phage display libraries, and/or high
throughput screening (e.g. developmental, practical or theoretical). Ancillary
subjects of key importance, such as robotics and informatics also covered.
Comparative
Biochemistry and Physiology - Part A: Molecular & Integrative
Physiology,
Elsevier, 1998- [earlier variant titles] http://www.elsevier.com/locate/cbpa
Molecular, cellular, integrative, and ecological physiology. Topics
include bioenergetics, circulation, development, excretion, ion regulation,
endocrinology, neurobiology, nutrition, respiration, and thermal biology. Study
on regulatory mechanisms at any level of organization such as signal
transduction and cellular interaction and control of behavior are also
published.
Comparative
Biochemistry and Physiology - Part B: Biochemistry & Molecular
Biology,
Elsevier, 1994- [earlier variant titles] http://www.elsevier.com/locate/cbpb
Covers biochemical and molecular biology aspects of metabolism, enzymology,
regulation, nutrition, signal transduction, promoters, gene structure and
regulation, metabolite and cell constituents, macromolecular structures,
adaptational mechanisms and evolutionary principles.
Comparative
Biochemistry and Physiology: Part C Toxicology and Pharmacology,
Elsevier, 2000- [earlier variant titles] http://www.elsevier.com/locate/cbpc
Concerned with chemical and drug action at different levels of organization,
biotransformation of xenobiotics, mechanisms of toxicity, including reactive
oxygen species and carcinogenesis, endocrine disruptors, natural products
chemistry, and signal transduction with a molecular approach to these
fields.
Current
Opinion in Chemical Biology, Elsevier, 1997- http://reviews.bmn.com/journals/atoz/latest?jcode=jchl
The subject of chemical biology is divided into nine major sections, each of
which is reviewed once a year.
Current Opinion in Drug
Discovery & Development, BioMedCentral, 1998- http://www.biomedcentral.com/curropindrugdiscovdevel/
http://www.biomedcentral.com/1367-6733
Bimonthly, focuses on the chemical aspects of drug discovery and development.
Journal of
Biological Chemistry, American Society Biochemistry Molecular Biology,
1905- http://www.jbc.org/
Papers based on original research that are judged, after editorial review, to
make a substantial contribution to the understanding of any area of biochemistry
or molecular biology. Impact 6.9
Journal of Biomolecular
Screening, SBS, 1996- http://www.sagepub.com/journal.aspx?pid=9162 Biomolecular interactions and the relevant underlying basic
sciences. The journal also offers practical applied information for the
design, development, implementation, and interpretation of new molecular
discovery approaches, methods, and screening technology.
Journal of
Combinatorial Chemistry, American
Chemical Society, 1999- http://pubs.acs.org/journals/jcchff/
Synthesis of chemical libraries, and methods for their analysis and screening,
studies that contribute to an understanding of high throughput synthesis. [more
in PDF]
Journal of
Lipid Research JLR, American Society of Biochemistry &
Molecular Biology, 1959- http://www.jlr.org/
Biology of lipids in health and disease. Regulation and mechanism of lipid function and metabolism, the genetic
regulation of lipid metabolism, and the clinical and nutritional
implications, emerging areas of genomics,
proteomics, and lipidomics. Covers biochemistry, cell biology, molecular
biology, structural biology, genetics, genomics, immunology, metabolism,
nutrition and clinical science as they relate to lipids.
Journal of Molecular
Recognition, Wiley http://www3.interscience.wiley.com/cgi-bin/jhome/13149
Molecular recognition phenomena
in biology refers to the non- covalent specific
interaction between two or more biological molecules exemplified by receptor-
ligand, antigen- antibody, DNA- protein, sugar- lectin and many other
interactions. Quantitative biomolecular interaction analysis using
biosensors and other solution or surface- mediated experimental techniques
including microcalorimetry. The design, synthesis
and application of structural or topological mimics of naturally occurring
molecules in the characterisation of molecular recognition processes, crystallography, NMR and site directed mutagenesis,
correlation between atomic structure and binding energy, improved computer simulation, docking and molecular design of
biologically active molecules. Applications of chemically and biologically generated molecular libraries to the
study of biomolecular interactions and the creation of novel functions.
Many analytical
and medicinal chemistry journals are also useful.
See
also Cheminformatics
journals
Aggregator
MDL's Discoverygate https://www.discoverygate.com/iss/servlet/App?Action=ShowApp
Search by any number of methods, including chemical structure.
Chemistry
News
American Chemical Society, Hot articles directory http://pubs.acs.org/hotartcl/index.html
See also Molecular
Diagnostics organizations clinical chemistry
Chemical
Terminology
Cheminformatics
journals organizations
terminology
Cheminformatics
definitions More
cheminformatics terminology Cheminformatics
overviews & introductions
Cheminformatics
Bibliographies
Gary Wigging, Chemical Informatics, Indiana Univ. http://www.indiana.edu/~cheminfo/informatics/cinformhome.html
Databases
3D databases, structures, substructures, docking databases,
ligand databases
Nucleic Acids Research annual
database issue See: Interactions,
genetic & molecular, Pathways, Molecular
Modeling, Proteins and Protein
structures See also Interactions, Sequences, Protein domains
(tertiary structures), Protein
families databases
QSAR & Modelling
Society databases Bioinformatics,
Biological collections, Biological effect data, Chemicals & drugs,
Environmental, Literature, Patents & Trademarks, QSAR http://www.ndsu.nodak.edu/qsar_soc/resource/database.htm
Cheminformatics
journals and newsletters
Chemical Informatics
Letters http://www.ch.cam.ac.uk/MMRG/CIL/
Jonathan A. Goodman, editor Latest news in chemical informatics, links to
relevant web sites, analysis and discussion.
Computational Biology and
Chemistry, Elsevier,
2003-
http://www.elsevier.com/inca/publications/store/6/2/7/3/2/0/
http://www.elsevier.com/locate/compbiolchem
All areas of computational life sciences. High quality research
contributions in the areas of nucleic acid and protein sequence research,
molecular evolution, molecular genetics (functional genomics and
proteomics),
theory and practice of either biology- specific or chemical- biology- specific
modeling, and structural biology of nucleic acids and proteins are particularly
welcome. Exceptionally high quality research work in bioinformatics, systems
biology, cybernetics, ecology, environmental sciences, computational
pharmacology, metabolism, biomedical engineering, epidemiology, and statistical
genetics will also be considered. Was Computers in Chemistry
International
Journal of Quantum Chemistry:
Theory and Computation in Chemistry, Physics, and Molecular Biology, Wiley,
1967- http://www3.interscience.wiley.com/cgi-bin/jhome/29830
Quantum mechanical
description of the structure and dynamics of atoms, molecules, and condensed
matter, embodies theoretical studies and computer simulations
of atomic and molecular systems and their interactions. Recent developments in molecular biology also call for new
applications where quantum mechanical components interface with molecular
mechanics and phenomenological modeling.
Interactions between the quantum and
statistical mechanical sub- disciplines of chemical physics. Reports of investigations that apply quantum based programs to
fundamental research and the interpretation of experimental data in the fields
of thermodynamics and chemical kinetics. Emphasis on formal and computational quantum
mechanics and its application to the theory and modeling of the structure and
dynamics of atoms, molecules, and condensed matter.
Journal of Chemical
Information and Computer Sciences JCICS , American Chemical Society,
1975- http://pubs.acs.org/journals/jcisd8/index.html
Research studies, programming innovations, and software and book
reviews to keep current with advances in this integral, multidisciplinary
field... database search systems, use of graph theory in chemical
problems, substructure search systems, pattern recognition and clustering,
analysis of chemical and physical data, molecular modeling, graphics and natural
language interfaces, bibliometric and citation analysis, and synthesis design
and reactions databases.
The new (as of Jan.
2004) JCICS editor plans a split into
two: one keeping JCICS's original
focus on chemical informatics and another anchoring reports in computational
chemistry. ACS has long needed a computational chemistry journal aligned
with the society's Division of Computers in Chemistry and the Theoretical
Chemistry Subdivision of the Division of Physical Chemistry. C&E News 81
(43) Oct. 27, 2003. The new journals, scheduled for launch in 2005, are
tentatively titled the Journal of Chemical Information & Modeling and
the Journal of Chemical Theory & Computation.
Journal of Computer
-Aided Molecular Design, Kluwer, 1987- http://www.kluweronline.com/issn/0920-654X
Information on both the theory and the application of computer-
based methods in the analysis and design of molecules. Scope encompasses: theoretical chemistry; computational chemistry; computer
and molecular graphics; molecular modeling; protein engineering; drug design;
expert systems; general structure-property relationships; molecular dynamics;
chemical database development and usage. Contributions on computer-aided
molecular modeling studies in pharmaceutical, polymer, materials and surface
sciences, as well as other molecular- based disciplines, are particularly welcome. A
number of issues per volume are dedicated to Perspectives in Drug
Discovery and Design, established to publish succinct overviews of current developments in the
multidisciplinary area of drug discovery and design.
Journal of Computational
Chemistry, Wiley, 1980- http://www3.interscience.wiley.com/cgi-bin/jhome/33822?CRETRY=1 All
aspects of computational chemistry: analytical, biological, inorganic, organic
and physical. Computational areas featured include ab initio and
semiempirical quantum mechanics, density functional theory, molecular mechanics,
molecular dynamics, statistical mechanics, cheminformatics, biomolecular
structure prediction, molecular design, and bioinformatics.
Journal of Molecular
Graphics and Modelling, Elsevier, 1997- http://www.elsevier.com/inca/publications/store/5/2/5/0/1/2/ Development and application of molecular
modelling in the study of molecular structure, function, interactions and
design. The journal publishes accounts of computational methods and research
results in all aspects of molecular modelling including computational chemistry,
protein and polymer engineering, pharmaceutical design, structural biology and
materials design.
Journal of Molecular
Modeling, Springer, 1995- http://www.ccc.uni-erlangen.de/jmolmod/
http://www.springerlink.com/app/home/journal.asp?wasp=4nc6tmxqlp4vfbg4w..
Focuses on "hardcore" modeling, publishes high quality science
including Life Science Modeling (including QSAR, data mining/ bioinformatics,
structure and substructure search), Materials Modeling, New Methods, and
Computational Chemistry in an interdisciplinary manner and within very short
publication times.
Cheminformatics blog
COSMAS:
Cheminformatics, Ontologies & Statistical Mining Aggregation Site http://www.methylsalicylate.com/cosmas/
.
Listservs
and websites
CCL.net Computational chemistry listserv http://ccl.net/
Topics which may appear on the list include: Reporting bugs in chemistry
software and possible work- arounds, New chemistry software announcements,
Announcements of computational chemistry- related workshops and symposia, New
methods and techniques in computational chemistry, Questions and answers about
solving computational chemistry problems, Programs and utilities, Information on
the availability of particular software, data, etc., Hardware- related issues
relevant to the computational chemistry community, Opinions about services and
products.
Cheminformatics.org http://www.cheminformatics.org/phplinks/index.php?PHPSESSID=146e54dc5...
Chminf-l Chemical Information
Sources List , 1991-
http://listserv.indiana.edu/archives/chminf-l.html
Building blocks,
biological pathways and networks, NIH Roadmap http://nihroadmap.nih.gov/buildingblocks/index.asp
Yahoo Cheminformatics http://groups.yahoo.com/group/cheminformatics/
Chemical
Informatics Organizations
Chemical Informatics Societies http://www.indiana.edu/~cheminfo/informatics/cinformsocs.html
2 ACS divisions and about 15 other groups (Not all links work 11/20/03]
Molecular Graphics
and Modelling Society http://www.mgms.org/
QSAR and Modelling
Society http://www.ndsu.nodak.edu/qsar_soc/index.htm
Chemical
Informatics Terminology
Other
Information resources Genomics,
proteomics Drug
discovery & development Chemical
genomics Toxicogenomics Bioinformatics
Cheminformatics
Technologies
Molecular
Medicine Business
What are genomics
and proteomics? chemical
genomics? pharmacogenomics? toxicogenomics?
What are bioinformatics?
cheminformatics? informatics?
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