ACS Organic Chem Links - American Chemical Society Organic Chemistry Web Links
ADME-AP - Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.
ADMET.net - The World of AMDE and Toxicology (information resource launch site)
Analytical Chemistry Springboard - This is an attempt to present a comprehensive list of analytical chemistry resources on the Internet.
Blue Obelisk Movement - The Internet has brought together a group of chemists/programmers/informaticians who find themselves working together using collaborative tools and sharing commonality of vision.
CACTVS - a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type
ChemDB - ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB.
ChEBI - Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.
ChemBank - ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.
ChemBioServer - MOTIVATION: ChemBioServer is a publicly available web-application for effectively mining and filtering chemical compounds used in drug discovery. It provides researchers with the ability to (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply perfect match substructure search, (iv) cluster compounds according to their physicochemical properties providing representative compounds for each cluster, (v) build custom compound mining pipelines and (vi) quantify through property graphs the top ranking compounds in drug discovery procedures. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.
Chemfinder - ChemFinder has been providing free chemical searching to hundreds of thousands of scientists since 1995. This free database includes: Chemical Structures (2D structures & 3D models), Physical Properties (MP, BP, CAS RN, & more) and Hyperlinks (Links to other websites with information about your compound)
Chemical Calculations - Multiple different tools for performing inorganic, organic and physical chemical calculations
Chemical Database - Hazardous Chemical Database
Chemical Thesaurus - Reaction chemistry database
ChemIDplus - This database allows users to search the NLM ChemIDplus database of over 370,000 chemicals. A user may enter compound identifiers such as Chemical Name, CAS Registry Number, Molecular Formula, Classification Code, Locator Code, and Structure or Substructure. New searchable features include search and display by Toxicity indicators such as Median Lethal Dose (LD50), by Physical/Chemical Properties such as LogP, and by Molecular Weight.
Chemindustry.com - A worldwide search engine for the chemical industry
Chemoinf.com - The purpose of this site is to provide learning tools, resources and pointers for further exploration in the developing field of chemoinformatics (also known as cheminformatics and chemical informatics), molecular modeling and computer-aided drug design.
Cheminformatics.org - All things chemoinformatics
Chemoinformatics Journals - Google list of links to chemoinfo journals
ChemMine - ChemMine is a compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens. The ChemMine project is divided into three main components: a compound database, a cheminformatic workbench and a screening database.
ChemSpider - a value-added offering of publicly available chemical structures since many additional properties have been added to each of the chemical structures
COPICAT - Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive computational methods to predict interactions between chemical compounds and proteins are needed for virtual screening of lead compounds. Previously, we proposed a novel method for predicting protein-chemical interactions using two-layer Support Vector Machine classifiers that require only readily available biochemical data, i.e. amino acid sequences of proteins and structure formulas of chemical compounds. In this article, the method has been implemented as the COPICAT web service, with an easy-to-use front-end interface. Users can simply submit a protein-chemical interaction prediction job using a pre-trained classifier, or can even train their own classification model by uploading training data. COPICAT's fast and accurate computational prediction has enhanced lead compound discovery against a database of tens of millions of chemical compounds, implying that the search space for drug discovery is extended by >1000 times compared with currently well-used high-throughput screening methodologies.
DrugBank - The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Drug Design and Metabolism Sites - Free and proprietary software packages to facilitate drug design
echeminfo - eCheminfo is a global Community of Practice (CoP) dedicated to the communication of research and development of best practices in cheminformatics and chemical modelling of relevance to drug discovery
eMolecules (Chmoogle) - Ready for a genuine cheminformatics system that searches for molecules using chemical structure? With eMolecules, just draw your chemical structure with your favorite molecule editor, then click "Go", and instantly search millions of molecules from across the Web and from chemical suppliers worldwide.
FAF-Drugs - In silico screening based on the structures of the ligands or of the receptors has become an essential tool to facilitate the drug discovery process but compound collections are needed to carry out such in silico experiments. It has been recognized that absorption, distribution, metabolism, excretion and toxicity (ADME/tox) are key properties that need to be considered early on, even during the database preparation stage. FAF-Drugs is an online service based on Frowns (a chemoinformatics toolkit) that allows users to process their own compound collections via simple ADME/Tox filtering rules such as molecular weight, polar surface area, logP or number of rotatable bonds. SMILES (Simplified Molecular Input Line Entry System), CANSMILES (canonical smiles) or SDF (structure data file) files are required as input and molecules that pass or do not pass the filters are sent back in CANSMILES format. This service should thus help scientists engaging in drug discovery campaigns. Other utilities and several compound collections suitable for in silico screening are available at our site.
GLIDA - G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GLIDA is a public GPCR-related Chemical Genomics database that is primarily focused on the integration of information between GPCRs and their ligands. It provides interaction data between GPCRs and their ligands, along with chemical information on the ligands, as well as biological information regarding GPCRs. These data are connected with each other in a relational database, allowing users in the field of Chemical Genomics research to easily retrieve such information from either biological or chemical starting points. GLIDA includes a variety of similarity search functions for the GPCRs and for their ligands. Thus, GLIDA can provide correlation maps linking the searched homologous GPCRs (or ligands) with their ligands (or GPCRs). By analyzing the correlation patterns between GPCRs and ligands, we can gain more detailed knowledge about their conserved molecular recognition patterns and improve drug design efforts by focusing on inferred candidates for GPCR-specific drugs. This article provides a summary of the GLIDA database and user facilities, and describes recent improvements to database design, data contents, ligand classification programs, similarity search options and graphical interfaces.
MODEL - for Computing structural and physichemical properties of molecules from their 3D structures
MolInspiration ToolKit - molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure search or similarity and pharmacophore similarity search. Our products support also fragment-based virtual screening, bioactivity prediction and data visualization. Molinspiration tools are written in Java, therefore are available practically on any computer platform.
NCI 3D Structure Database - The NCI DIS 3D database is a collection of 3D structures for over 400,000 drugs which was built and is maintained by the Developmental Therapuetics Program Division of Cancer Treatment, National Cancer Institute, Rockville ,MD. The database is an extension of the NCI Drug Information System
NIST Chemistry WebBook - This site provides thermochemical, thermophysical, and ion energetics data compiled by the National Institute of Standards and Technology (NIST) under the Standard Reference Data Program.
OCHEM - The OCHEM is an online database of experimental measurements integrated with the modeling environment. Submit your experimental data or use the data uploaded by other users to build predictive QSAR models for physical-chemical or biological properties.
Organic & Medicinal Chemistry Links - resources in Organic Chemistry and Medicinal Chemistry
OpenBabel - a format conversion tool for drugs
PreADME - a web-based application for predicting ADMET data and building drug-like library using in silico method.
PowerMV Molecular Viewer- National Institute of Statistical Sciences. A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
Predictive Toxicology Software
Pubchem - PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
Query Chem - Combine text and chemical structure Web searches
SENECA - A program package for Computer Assisted Structure Elucidation (CASE) of organic molecules. While it currently uses mainly 1D and 2D NMR spectroscopy for the CASE process it is open to all types of spectroscopic data.
sMOL Explorer - sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create personal databases by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools from Weka and R packages to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data and (4) building the classification model of biological activity.
Spectral Database of Organic Compounds - SDBS is an integrated spectral database system for organic compounds, which includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum.
SuperDrug Database - MOTIVATION: Different resources exist for experimentally determined and computed three-dimensional (3D)-structures of low molecular weight structures but for approved drugs, no free, publicly accessible source of 3D-structures and conformers is available. Furthermore, for selection purposes or for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemical (ATC) classification codes to each structure according to the WHO-scheme would be desirable. RESULTS: The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 10(5) structural conformers. Here we present a web-query system enabling searches for drug name, synonyms, trade name, trivial name, formula, CAS-number, ATC-code etc. 2D-similarity screening (Tanimoto coefficients) and an automatic 3D-superposition procedure based on conformational representation are implemented. Drug structures above a similarity threshold as well as superimposed conformers can be retrieved in the mol- file format via a graphical interface.
SuperHapten - The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6-10% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity.
USDA Phytochemical Database - Thousands of phytochemicals have been isolated and characterized from plants, including fruits and vegetables. The isolated phytochemicals are grouped into distinctive classes by the number and kind of constitutive atoms and the structure of the basic skeleton. This database enables to search phytochemicals by using their names or using a alphabetical list. The data page of each phytochemical contains its chemical structure, formula, and molecular weight.
WebAnalytes - Direct-to-the-resources Analytical Chemistry Web Directory