Curator Dashboard

Software toolkit of computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software is designed to work with biomolecules, nanostructures, and solid-state, from quantum to classical, and all combinations, ground and excited-states, Gaussian basis functions or plane-waves, scaling from one to thousands of processors, and the properties and relativistic effects of computational chemistry problems.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software program for semiempirical quantum chemistry for handling of biomolecules.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software program for electronic structure modeling that enables researchers to study and predict the properties of molecules and reactions under a wide range of conditions, especially those that are difficult or impossible to observe experimentally.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Ab initio molecular modeling software program that computes an array of molecular properties such as multipole moments, polarizabilities, and electrostatic potential. It can also map reaction coordinates between reactants, products, and transition states.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Collection of databases with standalone databases, which gives opportunity for customers to integrate the data into their internal tools and databases, as well as online databases, that are available to the customers from a dedicated website where an individual can query and export the data in the selected format. The standalone database topics include medicinal chemistry, drugs and target class based compounds. The online databases are comprised of three major compilations: GVK BIO Online Structure Activity Relation Database (GOSTAR), GVK BIO Biomarker Database (GOBIOM), and Clinical Trial Outcome Database (CTOD).

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

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.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen