JMol is a viewer of molecular structures but the JMol Editor can be used to alter atom positions or identities and to add/remove atoms.
Compound converter joins several Open Babel command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state & pH) others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).
OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures into SMILES or SDF. It generates the SMILES or SDF representation of any molecular structure image within a document which is parseable by ImageMagick.
OPSIN is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
Uses the Open Babel Obgrep to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
Parses a multiple molecules file and deletes any present counterions or fragments.
Filters a library of compounds and removes duplicated molecules comparing either InChI or SMI.
Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
Filters a library of compounds and removes small molecules below a predefined input number of atoms.
Spectrophores is a screening technology by Silicos which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of Spectrophores of different molecules.
Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar Spectrophores. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.
Simsearch is a chemfp tool searching a FPS file for similar fingerprints.
Substructure search is based on Open Babel FastSearch. FastSearch uses molecular fingerprints to prepare and search an index of a multi-molecule datafile. It allows fast substructure and structural similarity searching. The indexing is a slow process (~30 minutes for a 250,000 molecule file). The subsequent seaching is much faster, a few seconds, and so can be done interactively.
Computes several physico-chemical properties (e.g. logP, PSA, MW, etc.) for a set of molecules. Accepts SDF or MOL2 as input file as 3D coordinates of the molecules have to be provided.
Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
Parses a molecular file and removes the protonation state of every atom.
Changes the title of a molecule file to a metadata value of a given ID in the same molecule file.
Confab is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
Chemfp is a tool for fingerprint generation. It supports the FPS fingerprint file format using Open Babel, OpenEye and RDKit .
Read an input SDF file, extract the fingerprints and store them in a fps-file.
Describes the similarity of a compound to known drugs. Comes with three applicable varieties (QEDw,mo, QEDw,max, QEDw,u ).
An open source cheminformatics and machine learning toolkit with a lot of overlap with OpenBabel. It therefor can be used to compare results with OpenBabel. The tool offers different descriptor and fingerprint calculations.
Calculates the Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products.
Shape-it is a silicos-it tool that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of gaussian volumes as descriptor for molecular shape as it was introduced by Grant and Pickup.
Shape-it is a program that is instructed by means of command line options. The program expects a single reference molecule (with three-dimensional coordinates) and a database file containing one or more molecules (with three-dimensional coordinates) that need to be shape-aligned onto the reference molecule. The tool returns all aligned database molecules and their respective shape overlap scores, or the top-best scoring molecules.
Strip-it is a program by silicos-it that identifies and extracts predefined scaffolds from organic small molecules. The program is linked against the open source C++ library of Open Babel.
The program comes with a number of predefined molecular scaffolds for extraction. These scaffolds include, amongst others molecular frameworks as originally described by Bemis and Murcko, molecular frameworks and the reduced molecular frameworks as described by Ansgar Schuffenhauer and coworkers and scaffold topologies as described by Sara Pollock and coworkers.
Generates hierarchical clusters and visualises clusters with dendrograms. Accepts fingerprints in FPS format as input.
Taylor-Butina clustering is an unsupervised non-hierarchical clustering method which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. Fingerprints in FPS format are needed as input.
Splits a molecule on predefined spots, following the RECAP-rules.
Merges small molecules together to larger compounds using predefined reactions. The options Molecule dependend iteration depth and Number of repeats can be used to adjust the created number of compounds and the actual computation time.
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