Curator Dashboard

Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Database of marketed and developed drugs indexed with internationally-recognized drug names, synonyms, trade names, trivial names and trial preparation codes in one source, plus compound structures and activity data. Each record has chemical structure and is classified by drug activity, mechanism of action, treatment, manufacturer, synonyms, medical nformation and literature references.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software package that uses homology modeling and fold recognition to make protein structure predictions.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Pharmacophore modeling software to create 3D structure activity relationships, screen databases, and generate hits through establishing a chemical space occupied by active ligands. Used in drug design.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Drug and molecular design environment with tools for molecular modeling. It includes tools for small molecule and macromolecular modeling and simulation, cheminformatics, lead identification and lead optimization. Users can: perform multi-criteria drug design; predict safety issues and/or off-target pharmacology; identify leads using ligand-based or structure-based virtual screening, and chemical library design; and perform lead optimization using various QSAR methods.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Drug discovery platform for medicinal and computational researchers. Users can assess the binding affinity and contributions to binding of a complex, find new scaffolds, grow molecules towards pharmacophore points, link fragments, and investigate possible dock binding conformations.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Commercial organization which provides molecular modelling and cheminformatics software to the pharmaceutical industry.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Molecular graphics environment which provides biologists and chemists with representations of proteins, DNA, RNA, and multiple sequence alignments. Users can build, annotate, and edit interactive views and slides of molecules. Users can also superimpose protein structures, search PDB, measure distanaces and angles, and view and make high resolution images of alignments.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Core facility that provides access to genome-wide collections of cDNAs and siRNAs that can be used to interrogate cellular models of signal transduction pathways and phenotypes. Services include cell lines, hit-picking clones and various screening sets, and access to equipment.Provides instruments:Analyst Molecular Devices,Embla Molecular Devices, Envision Perkin Elmer, Platemate Matrix, Tecan M200, Wellmate Matrix.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Non-profit dedicated to conducting collaborative research to find cures for human disease, improve quality of life, and educate and train the next-generation of scientists. It is the overarching organization of more than a dozen core facilities that provide various resources in biomedical research.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Producer of antibodies for investigators to use as diagnostic tools and therapeutic reagents in their research studies. The center works in conjunction with the Department of Animal Resources, and is able to assist in all stages of both polyclonal and monoclonal antibody development.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen