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You are here > -Omics & Informatics main page > Information Resources: Chemical genomics, Cheminformatics DRAFT
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Bibliographies Guide to Selected
Biotechnology Resources at Stanford Univ., Swain Chemistry & Chemical
Engineering Library, 2003 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 Combinatorial and
Chemogenomics Journals 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/ 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 Chemistry
News See also Molecular Diagnostics organizations clinical chemistry Cheminformatics
journals organizations
terminology Cheminformatics definitions More cheminformatics terminology Cheminformatics overviews & introductions Cheminformatics
Bibliographies 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 Computational Biology and
Chemistry, Elsevier,
2003- 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 Listservs
and websites 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 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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