Search Results for "molecules"

SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).

Distribution of Solution Conformations (DISCON) is a software package designed for determining the major solution conformations of organic molecules or small peptides based on NMR experiments. Copyright 2011 University of Pennsylvania

Computationally predicts the pharmacokinetic properties of drug candidates using Quantitative Structure Property Relationships (QSPR) modelling. Assembles a set of tools and databases for predicting the physical properties of small molecules. The program models a given property's dependence on a collection of molecular and structural descriptors using a training set of molecules. Neural networks and support vector regression are available, as well as linear models. The models generated...

A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity...

Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).

Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However...

ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available...

Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.

Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection...

Calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen compound libraries and to design new lead compounds. Maven dependancy: <dependency> <groupId>uk.ac.ebi.cheminformatics</groupId> <artifactId>NP-Likeness</artifactId> <version>2.1</version> </dependency> Required repository: <repositories> <repository> ...

TreeLiker is a collection of fast algorithms for working with complex structured data in relational form. The data can, for example, describe large organic molecules such as proteins or groups of individuals such as social networks or predator-prey networks etc. The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem...

JTHERGAS (a JAVA implementation of THERGAS) estimates thermodynamic information from two dimensional graphical representations of molecules and radicals based on the Benson additivity method.

Nanodesigner is a software platform for research on molecular nanotechnology. It has a plug-in architecture and will include tools for molecular visualization & modelling, design of complex new molecules, molecular dynamics,...

The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.