Welcome to Chemoinformatics resources
The main goal of the OSDDlinux is to provides a platform for Bioinformatician, Biologists and students to provides basic infrastructure and tools related to chemoinformatics resources. Here we provided some commonly used tools and techniques used in chemoinformatics field.
On this portal user can find different resources related to chemoinformatics field from different groups:| Web services in chemoinformatics |
| Database | Description |
|---|---|
| PubChem | PubChem is a database of chemical molecules which maintains three types of information namely, substance, compound and BioAssays. |
| ZINC | ZINC database contains 21 million compounds available for virtual screening. In this database various molecule features like molecular weight, logP etc are included. |
| ChEMBL | This database provides comprehensive information about 1 million bioactive (small drug-like molecules) compounds with 8200 drug targets. |
| ChemDB | It is a database of five million chemicals which contains information of chemicals that include predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. |
| ChemSpider | ChemSpider contains more than 28 million unique chemical entities aggregated from more than 400 diverse data sources. |
| BindingDB | It is a binding affinity database of small molecules which contains 910,836 binding data, for 6,263 protein targets and 378,980 small molecules. |
| PDB-Bind | It is a collection of binding affinities for protein-ligand complexes with known three-dimensional structures. It contains 5671 protein-ligand complexes. |
| PDBeChem | It provides comprehensive information of ligands, small molecules and monomers. Presently it consists 15502 ligands. |
| KEGG | It is a database resource that integrates genomic, chemical and systemic functional information. |
| HMDB | A database containing detailed information about small molecule metabolites found in the human body. |
| SMPDB | It is Small molecule Pathway database that contains more than 350 small-molecule pathways found in humans. |
| BIAdb | It is a comprehensive database of benzylisoquinoline alkaloids which contains information about 846 unique benzylisoquinoline alkaloids. |
| DrugBank | The database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target ((i.e. sequence, structure, and pathway) information. The database contains 6712 drug entries including 1448 FDA-approved small molecule drugs, 131 FDA-approved biotech (protein/peptide) drugs, 85 nutraceuticals and 5080 experimental drugs. |
| HIT | HIT is a comprehensive database for protein targets for FDA-approved drugs as well as the promising precursors. It currently contains about 1,301 known protein targets (221 proteins are described as direct targets). |
| SuperNatural | A freely available database of approximately 50,000 natural compounds. |
| NPACT | It contains experimentally validated plant-derived natural compounds exhibiting anti-cancer activity. Currently it contains 1574 compound entries. |
| TTD | This database provides information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. |
| PharmaGKB | It is a pharmacogenomics knowledge resource that encompasses clinical information of drug molecules. |
| SuperDrug | This database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. |
| Molecular Editors |
| Softwares | Description |
|---|---|
| PubChem Sketcher | It is web-based tool for molecule sketching which is integrated in PubChem. |
| ChemSketch | It is chemical drawing package that allows users to draw chemical structures including organics, organometallics, polymers, and Markush structures. |
| JChemPaint | It is java-based software for drawing, editing and viewing 2D chemical structure. |
| BKchem | BKchem is python based 2D molecule editor. It allows users to draw, edit, visualize the molecules and provide various options to the users. |
| XDrawChem | It is a two-dimensional molecule drawing program. |
| MedChem Designer | It is used for drawing molecules and integration with ADMET property. |
| JME | It is a java based software for draw, edit, and view molecules. |
| Chemical clustering softwares |
| Softwares | Description |
|---|---|
| ChemMine | This tool performs clustering using three clustering algorithms: hierarchical, binning and multidimensional scaling. |
| ChemMineR | ChemMineR is a R based open-source tool that provides various functions for clustering entire compound libraries and visualizing clustering results and compound structures. |
| ChemBioserver | It is a free web-based application that performs the clustering by two methods, the hierarchical and the modern Affinity Propagation (\ AP) clustering algorithm. |
| Jcluster | ChemAxons JKlustor Suite used to search similarity, calculate diversity and structural comparison and chemical clustering based on the molecular descriptors. |
| Scafold Hunter | Scaffold Hunter is a freely available open source tool for chemical clustering, intuitive hierarchical structuring, visualization, analysis of complex structure, exploration of chemical space to identify scaffolds of compounds endowed with a desired activity. |
| Tools for Combinatorial chemistry/analogs generation |
| Softwares | Description |
|---|---|
| SmiLib | SmiLib is a freely available Linux based tool that can be used as command line and graphical user interface for generating combinatorial library. It requires three substructures: Scaffolds, Building blocks and Linkers to generate a combinatorial library. |
| CLEVER | Chemical Library Editing, Visualizing and Enumerating Resource (CLEVER) is a free tool that enumerates chemical libraries using customized fragments and used in computes the physicochemical properties of generated molecules. |
| GLARE | Global Library Assessment of REagents (GLARE) is an open source package to generate the combinatorial library. |
| Newlead | It is used for automatic generation of combinatorial library from bioactive conformations of reference molecules. |
| Library synthesizer | It is java based tool for chemical library enumeration and profiling. |
| ChemT | An open-source software tool that automates the process of preparing custom-made template-based chemical libraries. |
| AutoClickChem | It is used to produce large combinatorial libraries of compound models for use in virtual screens. |
| Descriptors calculation software |
| Software | Description |
|---|---|
| PaDEL | PaDEL is used to calculate molecular descriptors and fingerprints. The software currently calculates 863 descriptors (729 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. |
| PowerMV | It is Windows based software for statistical analysis, molecular viewing, descriptor generation, and similarity search. |
| Joelib | JOELib/JOELib2 tool can be used for calculating native value descriptors and atom property descriptors. |
| CDK | CDK is a java based descriptor calculation tool which calculates topological, geometrical, charge based and constitutional descriptors. |
| ODDesripotrs | It is Java-based user friendly tool that calculates molecular descriptor to be used to develop the model for QSAR/QSPR. |
| MODEL | MODEL calculates 3,778 molecular descriptors from following six categories: constitutional descriptors, electronic descriptors, physical chemistry properties, topological indices, geometrical molecular descriptors, and quantum chemistry. |
| Filter-it | Filter-it is used for calculating descriptors and filtering drug-like molecules. |
| AFGen | This tool can calculate the graph based properties of chemicals. It includes paths (PF), acyclic subgraphs (AF), and arbitrary topology subgraphs (GF) graph properties. |
| ISIDA-fragmentor | It calculates sub structural molecular fragment and ISIDA property labeled fragments from a Structure-Data File (SDF). |
| Tools used in Molecular Docking |
| Name | Description |
|---|---|
| AutoDock | It predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure |
| DOCK | predicts binding modes of small molecule-protein complexes |
| DOT | docks macromolecules, including proteins, DNA, and RNA |
| GRAMM | Protein-Protein Docking and Protein-Ligand Docking |
| ZDOCK | rigid-body docking program |
| Softwares of Pharmacophore |
| Softwares | Description |
|---|---|
| Pharmer | It is efficient pharmacophore tool for virtual screening and it takes only one pdb file at a time. |
| Pharmapper | It contains a database repository of about 7000 targets based pharmacophore models. Based on triangle hashing based method, it finds the best matching poses of input ligand against all known pharmacophore based models. |
| PharmaGist | PharmaGist is used for searching pharmacophore from a set of ligand molecules. It requires the set of ligands known to interact with a particular target without any prior knowledge of target structure. |
| Boomer | It is freely available pharmacokinetic drug monitoring. |
| ZincPharma | It is used for screening of zinc database. |
| PKfit | PKfit is a tool for pharmacokinetic modeling. |
| JPKD | It is therapeutic drug monitoring tool. |