Software to draw chemical structures
Plugins:
OOChemistry – JChemPaint plugin for OpenOffice, which allows to embed chemical molecules into ODF.
Chem4Word – Chemistry Add-in for Microsoft Word, which allows to tag chemical entities and change the representation (2D, common name, formular, …).
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Facile management of molecules, atoms, bonds, and conformers
Conformational and frame-of-reference coordinate transformations
Maximum common substructure and exact substructure searching
Extremely fast 2D similarity using LINGOS
Perception of aromaticity with multiple models
Chemical reaction parsing and processing
Tetrahedral and E/Z stereochemistry recognition
Ring perception and Kekulization
Molecular normalization and canonicalization
Multiconformer molecule handling
Support for residues and bases
Ability to store and recall generic primitives or user-defined objects on molecules, atoms, bonds, or conformers
Multiple file format handling: robust reading and specification-compliant writing of:
SMILES, SLN,
SDF,
MOL, MOL2,
PDB,
FASTA,
MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary.
Available in C++, Python & Java
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Graph based structure to modify molecular structures
Classes for getting the aromatic flags for atoms and bonds
Classes for getting the hybridisation of atoms
Descriptor calculation classes (I-State, E-State, Burden, …)
SMiles
ARbitrary
Target
Specification (
SMARTS) substructure search
Base classes for reading and writing molecular file formats
Support for
SMILES, Chemical Markup Language (
CML),
CACTVS's clear text format (CTX), POVRay export (including aromatic rings)
Atom and bond properties classes (including import and export filter)
Processes / External processes and process decision filters
Regression module using Neural Networks (
JavaNNS)
Regression module using Support Vector Machines
JOELib-Matlab connection, e.g. for feature extraction
External processing modules for 3D structure generation with
Corina and descriptor calculation with
Petra (especially atom and bond property descriptors).
Database module checking for duplicate molecules
Available in Java
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3D Rendering
Input/Output
CML,
SMILES parsing/generation,
MDL Molfile support (limited),
InChI (via JNI bridge), readers for XYZ, ShelX, HIN, GhemicalMM, Mol2
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rule based
IUPAC name parser
Virtual Screening
Modelling
3D model builder
atom typing
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Kabsch alignment
Chemical Graphs
Properties
Structure Generation
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Protein Structures
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Bio Events
Learning material
Blogs and forums
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Blue Obelisk Exchange – the place to ask about the use and development of Open Data, Open Source, and Open Standards
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Search engines and databases
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Reflect – Highlighting Proteins, and Small Molecule Names, similar to this:
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Chemical compound search
Text extraction and analysis
OSRA – a utility designed to convert graphical representations of chemical structures
Imago OCR – a toolkit for 2D chemical structure image recognition
Other
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Which Genes Can Be Patented? (isolated DNA could not be patented, but that synthetic DNA created in the laboratory — complementary DNA, or cDNA — could be protected under the patent laws)
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Bioclipse – a Rich Client for the Life Sciences
Features:
The management, analysis, and visualization of chemical structures and related information
The management and analysis of biological sequences (DNA, RNA, and proteins).
Pharmacological research and drug discovery.
Data analysis engine based on the statistical language R.
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