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admin | Category: Electile Dysfunction 2016 | 16.05.2015
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News Your Text Here• Your Text Goes here NEWS• Download this awesome diagram Your text goes here. News Your Text Here NEWS • • Your Text Goes here Download this awesome Your text goes here. Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services. These tools are classified according to their application field, trying to cover the whole drug design pipeline. Your Text Goes here.• Bring your presentation to Download this Download this life awesome diagram. Curated collection of commercially available chemical compounds, with 3D coordinates, provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). Free suite of multiconformational molecular databases for High-Throughput Virtual Screening.
Database of chemical compounds maintained by the National Center for Biotechnology Information (NCBI), along with bioassays results. The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Allows searching the ChemSpider chemical database, provided by the Royal Society of Chemistry. ZINClick is a database of triazoles generated using existing alkynes and azides, synthesizable in no more than three synthetic steps from commercially available products. Maximum Unbiased Validation Datasets for Virtual Screening, with non-clumpy, spatially random topology. Public, web-based informatics environment created by the Broad Institute's Chemical Biology Program. Collection created by selecting 1000 ligands from a one million compound library that were chosen to exhibit "drug-like" properties. Libraries of 30,184 (redundant) and 4,544 small-molecule fragments, all less than 150 daltons in weight, derived from FDA-approved compounds using the python script fragmentizer. Set of 239 molecules used for Absolute Solvation Free Energy calculations, in Maestro, SMILES and SMARTS format along with the experimental and calculated absolute solvation free energies. Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Relational database management system (RDBMS) data cartridge that provides fast, scalable, and efficient storage and searching solution for chemical information. Integrates structure handling and visualizing capabilities within a Microsoft Excel environment. Indigo-based utility for finding duplications and visual comparison of two files containing multiple structures. Databank of experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Subset of the Protein Data Bank (PDB), containing a collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature.
Collection of curated ligand-protein complexes, with 3D structures and experimental binding free energies.
Collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). Publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints and is completely scriptable through its application programming interface. The aim of PharmBench is to provide a community benchmark dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches, and also a webservice to help users evaluate their own methods. Data set of 53 high-quality protein-fragment complexes, filtered out from the Worldwide Protein Data Bank (wwPDB) and made publicly available. Collection of protein ligand complexes extracted fom the PDB along with biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. Public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Provides information on the abilities of drugs to interact with an expanding number of molecular targets. Free online repository of protein-ligand complexes which have been structurally resolved and thermodynamically characterised. 161 protein-ligand complexes with experimental and estimated binding free energies calculated with the BAPPL server. Dataset of DNA-drug complexes consisting of 16 minimized crystal structures and 34 model-built structures, along with experimental affinities, used to validate PreDDICTA. Set of 114 crystallographically determined protein-ligand structures used to test the docking program DOCK. Advanced chemical editor for drawing chemical structures, queries and reactions developed by ChemAxon. Tool of JChem for clustering, diversity calculations, and library comparisons based on molecular fingerprints and other descriptors. Chemical structure environment with a main focus on 2D graphics and publishing to create media for structures, reactions and spectra. Application for drawing publication-quality molecular structures and reactions, for iPhone and iPod Touch.
Chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet. Portable chemical dataset viewer for iPad, for browsing SAR reports, chemical catalogs, custom-made databases, and physical property references. Free open source software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS. Free and open source interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.


Free open source program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11. Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Can scan all data sources, including local files, remote files on network, emails, web pages, SharePoint contents, etc., and find contained chemical structures, and make them structure-searchable (substructure, full-structure, similarity). Free application to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile.
Allows creation and editing of molecules in browsers without Java support and without any plugins. Javascript libary you can display and draw chemical structures in web pages, which works cross browser, including IE, Firefox, Safari, Opera and Chrome, crose platform, including Window, Mac, Linux, and even iPhone, Android and other mobile devices. Open source, highly extensible program for interactive visualization and analysis of molecular structures and related data.
Program for 3D visualization of macromolecules, allowing to analyze several proteins at the same time. PyMOL plugins providing a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE).
Allows defining binding sites and export to Autodock and VINA input files, doing receptor and ligand preparation automatically, starting docking runs with Autodock or VINA from within the plugin, viewing grid maps generated by autogrid in PyMOL, handling multiple ligands and set up virtual screenings, and set up docking runs with flexible sidechains. Python module for dealing with structure files and trajectory data from the GROMACS molecular dynamics package. Free open source molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Free molecular visualization program for displaying proteins, DNA and RNA, and multiple sequence alignments. Integrated Front-End application for multiple structure visualization and multiple sequence alignment. Free open-source C++ library for molecular modelling, cheminformatics, and molecular visualization. Program for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
Free open source program for displaying, analyzing, editing, converting, and animating molecular systems (former JMolEditor). Includes interactions and functional effects of small molecules binding to their macromolecular targets, and series of drug discovery databases. Includes the conversion of chemical names to chemical structures, the generation of SMILES and InChI strings as well as the prediction of many physicochemical parameters.
It has single and multi conformer databases prepared for HTVS in different formats like Phase, Catalyst, Unity and SDF. It is currently the world's largest TCM database, and contains 170'000 compounds, with 3D mol2 and 2D cdx files, which passed ADMET filters.
Allows filtering by chemical supplier data (stock availability, price, delivery time, chemical suppliers, catalogs, minimum purity, etc.) and export the whole Mcule database including supplier and procurement related properties.
Database of 331,872 entries (268,246 unique SMILES), representing 1,966 unique targets, with bioactivity annotations. Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure.
Includes the analysis of chemical properties, such as ionization and tautomerization processes, and the in silico prediction of 24 important molecular properties in the biochemical profile of each structure. Mobile app, for iphone, ipad and android, which gives access to over 9 million molecules and 16 million chemical product variations offered by 56 different suppliers.
For each ligand in GLL, 39 decoys were drawn from ZINC ensuring physical similarity of six properties (molecular weight, formal charge, hydrogen bond donors and acceptors, rotatable bonds and logP), but structural dissimilarity.
Comprehensive and fully-edited database on natural products, arising from the Dictionary of Organic Compounds (DOC).The compilation of DNP is undertaken by a team of academics and freelancers who work closely with the in-house editorial staff at Chapman & Hall.
Includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data. Provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank.
The set includes a total of 667 fragments with accessible low energy ionization and tautomeric states and metal and state penalties for each compound from Epik. It has been developed giving special consideration to physicochemical properties and Lipinski's rule of five.
Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.
The database contains small molecule structures occurring as ligands in the Protein Data Bank. Freely available dictionary of molecular entities focused on a€?smalla€™ chemical compounds. Structures are fully supported within spreadsheets and be can viewed, edited, searched, resized, ordered, managed. All of the binding affinity data compiled in this database are cited from original references.
CREDO includes implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Non-commercial manually curated benchmarking database dedicated to the Nuclear Receptor(NR) ligands and structures pharmacological profiles. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. Provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters.
Maintained by the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute.
Database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. Interactive, visual database containing more than 350 small molecule pathways found in humans. DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Useful in combinatorial chemistry, drug design, or other areas where a large number of compounds need to be analyzed. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor.
The 3D editor allows addition, modification, replacement and deletion of atoms, bonds and groups, with Undo and Redo operations. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule.


Can send structure data via email, open structures from email or web, create graphical images or Microsoft Word documents with embedded structure graphics, calculate properties based on structures and use structures to search Mobile Reagents and ChemSpider. Exists as a Java stand alone application and two varieties of Java applet that can be integrated into web pages. Includes assignment of systematic names to organic structures according to IUPAC nomenclature rules, and drawing of molecules from IUPAC names.
It contains a GUI program and a command-line utility, as well as a documented API for developers. It shows the capabilities of the Dendro Chemical Editor control for Android to build chemistry-aware mobile applications. Includes unlimited structure based predictions for a range of properties (pKa, logD, namestructure, etc.). Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB). It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. Free, open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications (hosts, i.e. It is a comprehensive tool for user-friendly creation, 3D graphical design, display and manipulation of crystal and macro-molecular structures, surface or interfaces and defects and for the simulation of X-Ray, neutron and electron diffraction patterns. Provided by the Department of Pharmaceutical Sciences of the University of Modena and Reggio Emilia.
MMsINC supports various types of queries, including substructure queries and the novel 'molecular scissoring' query.
It contains a total 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target. These can be used for fragment docking, core hopping, lead optimization, de novo design, etc. Provided by the Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.
Its extensible indexing is designed to enable scientists to store, index, and search chemical moieties alongside numbers and text within one underlying relational database server. Files can contains large amount of molecules and ChemDiff was test on files with up to 1 million ones. The dataset is based on known pharmaceutically relevant co-crystallised protein ligand complexes, which were filtered to leave high-resolution structures containing drug-like small molecule ligands, for which electron density is also available. Provides experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. STITCH contains interactions for between 300,000 small molecules and 2.6 million proteins from 1133 organisms. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. The visualization of patterns is based on the visualization concept of the SMARTSviewer.Freely available for linux systems with 32 and 64 bit, windows 32bit systems and MacOS. Individual molecules, or whole datasheets, can be shared via iTunes or sent by email, using the standard MDL MOL and SDfile formats, which allows the data to be integrated into any external workflow. The table editor has many convenience features and data checking cues to make the data entry process as efficient as possible.
Recognizes structures, reactions and text from scanned images of printed chemistry literature and transforms the 'images' into a 'real structures' that can then be input into databases. WebME allows therefore web-based structure input also in institutions where Java applets are not allowed and offers complete platform compatibility.
Developed by the NIH resource for macromolecular modeling and bioinformatics, University of illinois. Blender, Cinema4D and Maya 2011) to provide simultaneous access the capabilities of all of the systems.
MMsINC is interfaced with other primary data collectors, such as PubChem, Protein Data Bank (PDB), the Food and Drug Administration database of approved drugs and ZINC.
It is possible to limit the search to specific suppliers, bookmark the search results, and export small sdfiles. Also includes 50 decoys for each active, having similar physico-chemical properties but dissimilar 2-D topology. A 3D superpositioning algorithm is implemented that allows to screen all ligands for possible scaffold hoppers as well as a 2D similarity screen for compounds based on fingerprints. For each target the structures have been aligned using the receptor backbone atoms, and then the ligands extracted and prepared by fixing their atom types and adding hydrogen atoms.
All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The actual molecule processing in WebME is based on the JMEPro editing engine running on a server. Allows converting a picture of a chemical structure taken from the iPhone camera into a structurally searchable molecule using OSRA (Optical Structure Recognition Application). DUD-E is provided freely by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
Provided by the Departments of Computing Science & Biological Sciences, University of Alberta. DS Visualizer ActiveX Control allows visualizing and interacting with molecules in Microsoft Office documents and Internet Explorer. DUD is provided freely by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). Download this • Your Text Goes hereawesome diagram.Bring yo ur • Download this awesomepresentation to life. Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized. B r i n g B r i n g Capture B r i n g • Capture your audience’s y o u r y o u r y o u r y o u r presentati presentati audience’s presentati attention on to life.
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