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Information resources: Combinatorial chemistry, chemogenomics and cheminformatics 

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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

Guide to Selected Biotechnology Resources at Stanford Univ., Swain Chemistry & Chemical Engineering Library, 2003

Open Directory Project OPD Biochemistry

Royal Society of Chemistry, Guide to Chemistry Resources on the Internet

Chemistry Databases
Chemical Abstracts  Gene sequences are indexed in Chem Abstracts, and assigned registry numbers. 

Combinatorial and Chemogenomics Journals
BMC Biochemistry, BioMedCentral, 2000-   All aspects of biochemistry, including metabolic pathways, enzyme functions, and small molecular components of cells and tissues

Biochimica et Biophysica Acta: 

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]  Application of chemistry to the investigation of biology and drug design.

ChemBioChem, Wiley, 2000-  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-  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-  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]  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]  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] 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- 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- Bimonthly, focuses on the chemical aspects of drug discovery and development.

Journal of Biological Chemistry, American Society Biochemistry Molecular Biology, 1905-  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- 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-  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- 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  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  

MDL's Discoverygate  Search by any number of methods, including chemical structure.

Chemistry News
American Chemical Society, Hot articles directory

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.

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

Cheminformatics journals and newsletters
Chemical Informatics Letters Jonathan A. Goodman, editor Latest news in chemical informatics, links to relevant web sites, analysis and discussion. 

Computational Biology and Chemistry, Elsevier, 2003-  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-  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- 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-  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- 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- 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-  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
Cheminformatics, Ontologies & Statistical Mining Aggregation Site .

Listservs and websites Computational chemistry listserv  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.

Chminf-l Chemical Information Sources List , 1991-

Building blocks, biological pathways and networks, NIH Roadmap

Yahoo Cheminformatics

Chemical Informatics Organizations
Chemical Informatics Societies 2 ACS divisions and about 15 other groups (Not all links work 11/20/03]

Molecular Graphics and Modelling Society

QSAR and Modelling Society 

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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