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 Awesome Cheminformatics !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
 Awesome Cheminformatics !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
▐ Cheminformatics (also known as chemoinformatics, chemioinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry.— 
▐ Wikipedia (https://en.wikipedia.org/wiki/Cheminformatics)
▐ Cheminformatics (also known as chemoinformatics, chemioinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry.— Wikipedia 
▐ (https://en.wikipedia.org/wiki/Cheminformatics)
A curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to contribute (CONTRIBUTING.md) !
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⟡ Jmol (http://jmol.sourceforge.net/) - Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.
⟡ VMD (http://www.ks.uiuc.edu/Research/vmd/) - Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
⟡ Chimera (https://www.cgl.ucsf.edu/chimera/) - Highly extensible program for interactive molecular visualization and analysis. Source (https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html) is available.
⟡ ChimeraX (https://www.cgl.ucsf.edu/chimerax/) - The next-generation molecular visualization program, following UCSF Chimera. Source is available here 
(https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html).
⟡ DataWarrior
 (http://www.openmolecules.org/datawarrior/index.html) - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
⟡ ChimeraX (https://www.cgl.ucsf.edu/chimerax/) - The next-generation molecular visualization program, following UCSF Chimera. Source is available here (https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html).
⟡ DataWarrior (http://www.openmolecules.org/datawarrior/index.html) - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
Command Line Tools
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General Purpose
⟡ RDKit (http://www.rdkit.org/) - Collection of cheminformatics and machine-learning software written in C++ and Python.
⟡ Indigo (https://github.com/epam/Indigo) - Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and 
Python wrappers.
⟡ Indigo (https://github.com/epam/Indigo) - Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.
⟡ CDK (Chemistry Development Kit) (https://sourceforge.net/projects/cdk/) - Algorithms for structural chemo- and bioinformatics, implemented in Java.
⟡ ChemmineR (https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html) - Cheminformatics package for analyzing drug-like small molecule data in R.
⟡ ChemPy (https://github.com/bjodah/chempy) - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
⟡ MolecularGraph.jl (https://github.com/mojaie/MolecularGraph.jl) - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
⟡ datamol (https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
⟡ CGRtools (https://github.com/cimm-kzn/CGRtools) - Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with 
backward compatibility to RDKit and NetworkX.
⟡ CGRtools (https://github.com/cimm-kzn/CGRtools) - Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with backward compatibility to
RDKit and NetworkX.
Format Checking
⟡ ChEMBL_Structure_Pipeline (formerly standardiser)
 (https://github.com/chembl/ChEMBL_Structure_Pipeline) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
⟡ ChEMBL_Structure_Pipeline (formerly standardiser) (https://github.com/chembl/ChEMBL_Structure_Pipeline) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
⟡ MolVS (https://github.com/mcs07/MolVS) - Molecule validation and standardization based on RDKit (http://www.rdkit.org/).
⟡ rd_filters (https://github.com/PatWalters/rd_filters) - A script to run structural alerts using the RDKit and ChEMBL
⟡ pdb-tools (https://github.com/haddocking/pdb-tools) - A swiss army knife for manipulating and editing PDB files.
@@ -129,8 +125,7 @@
⟡ PubChemPy (http://pubchempy.readthedocs.io) - Python wrapper for the PubChem PUG REST API.
⟡ ChemSpiPy (http://chemspipy.readthedocs.org) - Python wrapper for the ChemSpider API.
⟡ CIRpy (http://cirpy.readthedocs.org/) - Python wrapper for the NCI Chemical Identifier Resolver (CIR) (https://cactus.nci.nih.gov/chemical/structure).
⟡ Beaker (https://github.com/chembl/chembl_beaker) - RDKit (http://www.rdkit.org/) and OSRA (https://cactus.nci.nih.gov/osra/) in the Bottle (http://bottlepy.org/docs/dev/) on Tornado 
(http://www.tornadoweb.org/en/stable/).
⟡ Beaker (https://github.com/chembl/chembl_beaker) - RDKit (http://www.rdkit.org/) and OSRA (https://cactus.nci.nih.gov/osra/) in the Bottle (http://bottlepy.org/docs/dev/) on Tornado (http://www.tornadoweb.org/en/stable/).
⟡ chemminetools (https://github.com/girke-lab/chemminetools) - Open source web framework for small molecule analysis based on Django.
⟡ ambit (http://ambit.sourceforge.net/) - offers chemoinformatics functionality via REST web services.
@@ -179,8 +174,8 @@
⟡ Learncheminformatics.com (http://learncheminformatics.com/) - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
⟡ Python for chemoinformatics (https://github.com/Mishima-syk/py4chemoinformatics)
⟡ TeachOpenCADD (https://github.com/volkamerlab/TeachOpenCADD) - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
⟡ Cheminformatics OLCC (https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_(2019)) - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) 
course of University of Arkansas at Little Rock by Robert Belford
⟡ Cheminformatics OLCC (https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_(2019)) - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of 
Arkansas at Little Rock by Robert Belford
⟡ BigChem (http://bigchem.eu/alllectures) - All lectures of BigChem (http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
⟡ Molecular modeling course (https://dasher.wustl.edu/chem478/) - by Dr. Jay Ponder (https://dasher.wustl.edu/), a professor from WashU St.Louis.
⟡ Simulation in Chemistry and Biochemistry (https://dasher.wustl.edu/chem430/) - by Dr. Jay Ponder (https://dasher.wustl.edu/), a professor from WashU St.Louis.
@@ -191,11 +186,10 @@
⟡ PubChem Blog (https://pubchemblog.ncbi.nlm.nih.gov/) - News, updates and tutorials about PubChem (https://pubchem.ncbi.nlm.nih.gov/).
⟡ The ChEMBL-og blog (http://chembl.blogspot.tw/) - Stories and news from Computational Chemical Biology Group at EMBL-EBI (https://www.ebi.ac.uk/).
⟡ ChEMBL blog (http://chembl.github.io/) - ChEMBL on GitHub.
⟡ SteinBlog (http://www.steinbeck-molecular.de/steinblog/) - Blog of Christoph Steinbeck (http://www.steinbeck-molecular.de/steinblog/index.php/about/), who is the head of cheminformatics and metabolism at the 
EMBL-EBI.
⟡ SteinBlog (http://www.steinbeck-molecular.de/steinblog/) - Blog of Christoph Steinbeck (http://www.steinbeck-molecular.de/steinblog/index.php/about/), who is the head of cheminformatics and metabolism at the EMBL-EBI.
⟡ Practical Cheminformatics (http://practicalcheminformatics.blogspot.com/) - Blog with in-depth examples of practical application of cheminformatics.
⟡ So much to do, so little time - Trying to squeeze sense out of chemical data (http://blog.rguha.net/) - Bolg of Rajarshi Guha (http://blog.rguha.net/?page_id=8), who is a research scientist at NIH Center for 
Advancing Translational Science.
⟡ So much to do, so little time - Trying to squeeze sense out of chemical data (http://blog.rguha.net/) - Bolg of Rajarshi Guha (http://blog.rguha.net/?page_id=8), who is a research scientist at NIH Center for Advancing Translational 
Science.
   Some old blogs 1 (https://rguha.wordpress.com/) 2 (http://www.rguha.net/index.html).
⟡ Noel O'Blog (http://baoilleach.blogspot.tw/) - Blog of Noel O'Boyle (https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.
⟡ chem-bla-ics (http://chem-bla-ics.blogspot.tw/) - Blog of Egon Willighagen (http://egonw.github.io/), who is an assistant professor at Maastricht University.
@@ -208,16 +202,14 @@
⟡ Is life worth living? (https://iwatobipen.wordpress.com/) - Some examples for cheminformatics libraries.
⟡ Cheminformatics 2.0 (https://cheminf20.org/) - Blog of Alex M. Clark (https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery.
⟡ Depth-First (https://depth-first.com/) - Blog of Richard L. Apodaca (https://depth-first.com/about/), a chemist living in La Jolla, California.
⟡ Cheminformania (https://www.cheminformania.com) - Blog of Ph.D, Esben Jannik Bjerrum (https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a Machine Learning and AI 
specialists at AstraZeneca.
⟡ Cheminformania (https://www.cheminformania.com) - Blog of Ph.D, Esben Jannik Bjerrum (https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.
Books
⟡ Computational Approaches in Cheminformatics and Bioinformatics
 (https://books.google.com/books/about/Computational_Approaches_in_Cheminformat.html?id=bLqV4rYQoYsC) - Include insights from public (NIH), academic, and industrial sources at the same time.
⟡ Chemoinformatics for Drug Discovery (https://onlinelibrary.wiley.com/doi/book/10.1002/9781118742785) - Materials about how to use Chemoinformatics strategies to improve drug discovery results.
⟡ Molecular Descriptors for Chemoinformatics
 (https://onlinelibrary.wiley.com/doi/book/10.1002/9783527628766) - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.
⟡ Molecular Descriptors for Chemoinformatics (https://onlinelibrary.wiley.com/doi/book/10.1002/9783527628766) - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.
See Also