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3D-e-Chem-VM

Integrates cheminformatics and bioinformatics tools for the analysis of protein‚ąíligand interaction data. 3D-e-Chem-VM is an open source, freely available Virtual Machine that consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

UNICON

Encapsulates an important conversion functionality from the NAOMI software library in a single command-line tool. UNICON is a consistent chemical model that aims for the appropriate representation of molecules and an intuitive user interface. This module allows the combination of file format conversion and enumeration steps in a single run preventing piping of molecules through different tools, which minimizes the probability of processing errors. UNICON is part of the AMD tools software bundle.

WebCDK / Web Chemistry Development Kit

Facilitates the implementation of software packages in chemoinformatics. The CDK is an open-source Java library uses as the basis for other open-source projects. Besides its proven usability in research and production quality scientific software, the CDK has also become a valuable tool for teaching chemoinformatics. The functionality is provided for many areas in cheminformatics including molecule and reaction valence bond representation, canonical identifiers for fast exact searching and many others.

Octopus

Performs docking simulations of an unlimited number of compounds into a set of molecular targets. Octopus can carry out geometry refinement using the semi-empirical method PM7. It reduces the number of biological assays needed to determine a pharmacological mechanism. The tool can run automatically, although computational chemists are still needed to visually inspect the intermolecular interactions. It provides a second chance to find a use for these compounds as lead compounds.

LiSIs / Life Sciences Informatics

Facilitates the discovery of cancer chemopreventive agents. LiSIs uses numerous methods like RDKit, R or AutoDock Vina. It can proceed a lot of operations such as molecular descriptor calculation, predictive model generation and docking experiments. The tool enables the consideration of multiple pharmaceutically important properties to Virtual Screening (VS) and other library design experiments. It permits to drug discovery researchers to use state-of-the-art computational techniques on an easy way.

ODDT / Open Drug Discovery Toolkit

Aims to fulfill the need for comprehensive and open source drug discovery software. ODDT was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. It reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible.

Seurat

Streamlines data access and analysis from a broad mixture of in-house and in licensed databases, reports, literature, and computational results by providing a wide array of tools for medicinal chemists, biologists, modelers, and Information Technology (IT) professionals. Seurat is optimized specifically for small molecule screening, hit-to-lead, lead optimization, and preclinical analysis. This tool can: (1) Compound and assay registration; (2) Search and query chemical, physical, and biological properties; (3) Elevate hits to leads, lead optimization, and pharmacokinetics (PK) analyses, and more.

CVSP / Chemistry Validation and Standardization Platform

Obsolete
Validates and standardizes chemical structure representations. CVSP uses a set of systematic rules to proceed. It assists and encourages the processing of chemical structure files in order to offer more homogeneous compound representations for exchange and interchange between online databases. The tool has been applied to the analysis of small datasets of the order of a few thousand records. It has permitted to establish a recommended rule set.