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2023 ChemInformatics & Computational Chemistry

Coding in Cheminformatics

Cheminformatics & Green Chemistry

Cheminformatics vs BioInformatics

Computational Chemistry & Future of Medicine

Computational Chemistry  -Dr Grimme

One of the most cited Chemists -Dr. Houk

SeeSAR Drug Discovery with Midas

2023 CHEMINFORMATICS AND COMPUTATIONAL CHEMISTRY

 

 

COMPUTATIONAL CHEMISTRY PLAYLIST (68 VIDEOS)

https://www.youtube.com/watch?v=YF-amZgE2h4&list=PLm8ZSArAXicIWTHEWgHG5mDr8YbrdcN1K

 

PYTHON FOR COMPUTATIONAL CHEMISTRY PLAYLIST

https://www.youtube.com/watch?v=Sno4szlS4lw&list=PLhYF9QNr23IZ_bnrCIPdWdxNI_Ggl4m3G

 

MDTRAJ TUTORIAL - MOLECULAR TRAJECTORIES

https://www.youtube.com/watch?v=sDdB6ue03pI&list=PLhYF9QNr23IaE8tDPgF5dF1vLAgWYc_JK

 

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CHEMINFORMATICS TOOLS

 

  1. ToxRead

    • Website URL: https://www.vegahub.eu/portfolio-item/toxread/

    • Description: ToxRead is a free and open-source software tool for predicting the toxicity of chemicals. It uses various cheminformatics methods, including machine learning, to predict chemical toxicity based on their structure.
       

  2. ECOSAR

     

  3. ChemSpider (Same as in the previous lists)

    • Website URL: ChemSpider

    • Description: ChemSpider is a chemical structure database with over 100 million chemical structures and properties. It also provides various tools for green chemistry cheminformatics, allowing users to search for chemicals based on their green chemistry metrics and find sustainable alternatives.
       

  4. PubChem (Same as in the previous lists)

    • Website URL: PubChem

    • Description: PubChem is a free online database of chemical structures and properties, maintained by the National Center for Biotechnology Information (NCBI). It offers tools for green chemistry cheminformatics, enabling users to search for chemicals by their green chemistry metrics and identify sustainable alternatives.


 

MORE CHEMIFORMATICS TOOLS

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  1. Gaussian:

    • Description: Gaussian is a general-purpose quantum chemistry program that is widely used for electronic structure calculations, molecular dynamics simulations, and spectroscopy simulations.

    • Website: Gaussian, Inc.
       

  2. GAMESS:

    • Description: GAMESS is another general-purpose quantum chemistry program similar to Gaussian, capable of performing electronic structure calculations and molecular simulations.

    • Website: GAMESS-US
       

  3. Q-Chem:

    • Description: Q-Chem is known for its high accuracy and efficiency in quantum chemistry calculations, making it a popular choice for various research applications.

    • Website: Q-Chem, Inc.
       

  4. Molpro:

    • Description: Molpro is a quantum chemistry program specializing in handling large molecules and complex calculations, making it suitable for a wide range of research needs.

    • Website: Molpro Home Page
       

  5. NWChem:

  6. CP2K:

    • Description: CP2K is known for its versatility in modeling various systems, including molecules, materials, and surfaces, and it's highly regarded for its accuracy.

    • Website: CP2K - Open Source Molecular Dynamics
       

  7. VASP:

    • Description: VASP is a quantum chemistry program recognized for its precision and ability to model large systems, making it invaluable in materials research.

    • Website: The VASP Software
       

  8. ABINIT:

    • Description: ABINIT is designed for modeling complex systems, such as solids and liquids, and is well-regarded for its performance and versatility.

    • Website: ABINIT Homepage
       

  9. FHI-aims:

  10. ADF:

    • Description: ADF (Amsterdam Density Functional) is known for its ability to model relativistic effects in quantum chemistry, making it a valuable tool for specific research needs.

    • Website: Amsterdam Density Functional (ADF)

       

Popular molecular dynamics simulation programs using MDTraj and Python:
 

  1. Amber:

    • Description: Amber is a molecular dynamics simulation program known for its accuracy and its capability to model large systems.

    • Website: Amber Molecular Dynamics Software
       

  2. GROMACS:

  3. LAMMPS:

    • Description: LAMMPS is known for its scalability and flexibility, allowing it to handle a wide range of molecular dynamics simulations.

    • Website: LAMMPS Molecular Dynamics Simulator
       

  4. OpenMM:

 

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COMPUTATIONAL CHEMISTRY ALGORITHM DATABASES

 

  1. Chemistry Algorithms Database

    Website URL: Chemistry Algorithms Database

    Description: The Chemistry Algorithms Database is a resource that provides algorithms and software tools for various chemistry-related computations and data analysis.
     

  2. Open Reaction Database

    Website URL: Open Reaction Database

    Description: The Open Reaction Database is a platform for sharing and accessing chemical reaction data. It allows researchers to collaborate and access a wealth of reaction information.
     

  3. Organic Chemistry Algorithm Database

    Website URL: Organic Chemistry Algorithm Database

    Description: The Organic Chemistry Algorithm Database offers a collection of algorithms and tools specifically tailored for organic chemistry, including structure elucidation and reaction prediction.
     

  4. ChemSpider (Same as in the previous list)

    Website URL: ChemSpider

    Description: ChemSpider is a chemical structure database that allows you to search for information about chemical compounds. It provides access to a vast amount of chemical data.
     

  5. PubChem

    Website URL: PubChem

    Description: PubChem is a free chemistry database provided by the National Center for Biotechnology Information (NCBI). It offers information on the properties and biological activities of small molecules.
     

  6. NIST Chemistry WebBook

    Website URL: NIST Chemistry WebBook

    Description: The NIST Chemistry WebBook is an extensive online resource that provides chemical and physical property data, thermodynamic data, and spectral information for various compounds.
     

  7. Open Babel

    Website URL: Open Babel

    Description: Open Babel is an open-source chemical toolbox that allows users to convert, analyze, and manipulate chemical data and files. It provides a wide range of chemical file format support.
     

  8. RDKit

    Website URL: RDKit

    Description: RDKit is an open-source cheminformatics software toolkit designed for chemists and researchers. It offers tools for cheminformatics, including molecule handling and analysis.
     

  9. Psi4

    Website URL: Psi4

    Description: Psi4 is an open-source quantum chemistry software suite that provides a wide range of electronic structure methods and capabilities for computational chemistry research.
     

  10. NWChem

    Website URL: NWChem

    Description: NWChem is an open-source computational chemistry package designed for high-performance molecular electronic structure calculations. It is widely used for research in theoretical and computational chemistry.

     

  11. GitHub - hsiaoyi0504/awesome-cheminformatics: A curated list of Cheminformatics libraries and software.
     

  12. RDKit: RDKit is a free and open-source cheminformatics software library for the Python programming language. It provides a variety of cheminformatics functionality, including molecule parsing, chemical structure manipulation, molecular property prediction, and machine learning.
     

  13. MayaChemTools: Home: MayaChemTools is a free and open-source cheminformatics software library for the Python programming language. It provides a variety of cheminformatics functionality, including molecule visualization, chemical structure manipulation, and molecular property prediction.
     

  14. Chemistry Development Kit (CDK): CDK is a free and open-source cheminformatics software library for the Java programming language. It provides a variety of cheminformatics functionality, including molecule parsing, chemical structure manipulation, molecular property prediction, and machine learning.
     

  15. PaDEL-Descriptor: PaDEL-Descriptor is a free and open-source software package for calculating molecular descriptors. It provides a variety of molecular descriptors, which can be used for tasks such as molecular property prediction and machine learning.

  16. GitHub - ecrl/padelpy: A Python wrapper for PaDEL-Descriptor software.
     

  17. ChemDB Web Interface Index: ChemDB Web Interface is a free online cheminformatics database and web interface. It provides access to a variety of chemical data, including chemical structures, properties, and reactions.
     

  18. ChemPlot: A python library for chemical space visualization — ChemPlot 1.2.1 documentation: ChemPlot is a free and open-source Python library for chemical space visualization. It provides a variety of tools for visualizing chemical data, including scatter plots, heatmaps, and 3D visualizations.
     

  19. Visualization of very large high-dimensional data sets as minimum spanning trees | Journal of Cheminformatics | Full Text: This research paper describes a new method for visualizing very large high-dimensional data sets using minimum spanning trees.
     

  20. scikit-learn: machine learning in Python — scikit-learn 1.3.2 documentation: scikit-learn is a free and open-source Python library for machine learning. It provides a variety of machine learning algorithms, which can be used for tasks such as classification, regression, and clustering.
     

  21. GitHub - mojaie/MolecularGraph.jl: MolecularGraph.jl is a free and open-source Julia library for graph-based molecule modeling. It provides a variety of tools for manipulating and analyzing molecular graphs.
     

  22. GitHub - JuliaMolSim/AtomsBase.jl: AtomsBase.jl is a free and open-source Julia library for abstracting atomic structures. It provides a common interface for working with atomic structures, regardless of the specific implementation.
     

  23. GitHub - Chemellia/ChemistryFeaturization.jl: ChemistryFeaturization.jl is a free and open-source Julia library for featurizing atomic structures. It provides a variety of tools for converting atomic structures into feature vectors, which can then be used for machine learning tasks.
     

  24. GitHub - caseykneale/OpenSMILES.jl: OpenSMILES.jl is a free and open-source Julia library for parsing OpenSMILES strings. OpenSMILES is a chemical string notation that can be used to represent chemical structures.
     

  25. GitHub - simonster/Synchrony.jl: Synchrony.jl is a free and open-source Julia library for calculating coherence and phase-locking statistics. This can be useful for tasks such as analyzing molecular dynamics simulations.
     

  26. Welcome to the ChemML’s documentation! — ChemML documentation: ChemML is a free and open-source software library for machine learning in chemistry and materials science. It provides a variety of tools for tasks such as molecular property prediction, molecular design, and materials discovery.
     

  27. GitHub - hachmannlab/chemml: ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
     

  28. GitHub - Mariewelt/OpenChem: OpenChem is a deep learning toolkit for computational chemistry and drug design research. It provides a variety of tools for tasks such as predicting molecular properties, generating molecular structures, and screening for drug candidates.
     

  29. GitHub - chainer/chainer-chemistry: Chainer Chemistry is a library for deep learning in biology and chemistry. It provides a variety of tools for tasks such as predicting molecular properties, generating molecular structures, and screening for drug candidates.
     

  30. e-Drug3D: e-Drug3D is a software package for drug discovery. It provides a variety of tools for tasks such as molecular docking, virtual screening, and molecular dynamics simulations.
     

  31. Drug Design or Screen: Drug Design or Screen is a web service for drug discovery. It provides a variety of tools for tasks such as molecular docking, virtual screening, and molecular dynamics simulations.
     

  32. Shape-based alignment using SenSaaS: Shape-based alignment using SenSaaS is a web service for aligning molecules based on their shape. This can be useful for tasks such as comparing molecular structures and identifying similar molecules.
     

  33. pharmit: pharmit is a software package for interactive exploration of chemical space. It provides a variety of tools for visualizing and analyzing chemical data.
     

  34. Best Open Source Linux Chemistry Software 2023: This article lists a variety of free and open-source chemistry software packages for Linux.
     

  35. PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands | Journal of Chemical Information and Modeling: PSW-Designer is an open-source computational platform for the design and virtual screening of photopharmacological ligands. It provides a variety of tools for designing new photopharmacological ligands, predicting their properties, and screening them for activity against specific targets.
     

  36. (PDF) DataWarrior, An Open-Source Program For Chemistry Aware Data Visualization And Analysis: DataWarrior is an open-source program for chemistry-aware data visualization and analysis. It provides a variety of tools for tasks such as visualizing chemical data, identifying patterns in chemical data, and generating hypotheses.


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COMPUTATIONAL CHEMISTRY ALGORITHM RESOURCES
 

 

 

EXAMPLES OF COMPUTATIONAL CHEMISTRY ALGORITHMS

 

Ab initio algorithms:
 

  • Hartree-Fock (HF)

  • Configuration interaction (CI)

  • Coupled-cluster (CC)

  • Møller-Plesset perturbation theory (MPn)

  • Quantum Monte Carlo (QMC)
     

Density functional theory (DFT) algorithms:
 

  • Local density approximation (LDA)

  • Generalized gradient approximation (GGA)

  • Hybrid functionals

  • Meta-GGAs

  • Perdew-Burke-Ernzerhof (PBE) functional

  • Becke-Lee-Yang-Parr (BLYP) functional

  • B3LYP functional

  • ωB97X functional

  • M06-2X functional
     

Semi-empirical algorithms:
 

  • AM1

  • PM3

  • MNDO

  • CNDO/2
     

Molecular mechanics algorithms:
 

  • Molecular mechanics with generalized Born surface (MM-GBSA)

  • Molecular mechanics with Poisson-Boltzmann surface (MM-PBSA)

  • Molecular mechanics with implicit solvent (MM-IS)

  • Molecular mechanics with explicit solvent (MM-ES)
     

Monte Carlo algorithms:
 

  • Metropolis-Hastings algorithm

  • Gibbs sampling

  • Umbrella sampling

  • Free energy perturbation (FEP)

  • Thermodynamic integration (TI)
     

Quantum Monte Carlo algorithms:
 

  • Variational Monte Carlo (VMC)

  • Diffusion Monte Carlo (DMC)

  • Fixed-node diffusion Monte Carlo (FNDMC)
     

Other algorithms:
 

  • Path integral molecular dynamics (PIMD)

  • Hybrid quantum-mechanical/molecular mechanical (QM/MM) methods

  • Reaction path analysis (RPA)

  • Transition state theory (TST)

  • Statistical rate theory (SRT)

 

 

OPEN SOURCE COMPUTATIONAL CHEMISTRY TOOLS

 

  1. NWChem: https://www.nwchem-sw.org/
     

  2. PSI4: https://psicode.org/
     

  3. GAMESS: https://www.msg.chem.iastate.edu/gamess/
     

  4. ORCA: https://en.wikipedia.org/wiki/Orca
     

  5. VASP: https://www.vasp.at/
     

  6. FHI-aims: https://fhi-aims.org/
     

  7. Quantum ESPRESSO: https://www.quantum-espresso.org/
     

  8. LAMMPS: https://www.lammps.org/
     

  9. GROMACS: https://www.gromacs.org/


 

COMPUTATIONAL CHEMISTRY TOOLS EXPLAINED

 

  1. NWChem: NWChem is a general-purpose computational chemistry package that can be used to perform a wide range of calculations, including quantum mechanics, molecular mechanics, and dynamics simulations.
     

  2. PSI4: PSI4 is another general-purpose computational chemistry package. It is known for its speed and accuracy, and it is widely used by researchers in academia and industry.
     

  3. GAMESS: GAMESS is a quantum chemistry package that is known for its flexibility and ease of use. It is widely used by researchers in academia to study the properties of molecules and materials.
     

  4. ORCA: ORCA is a quantum chemistry package that is known for its accuracy and efficiency. It is widely used by researchers in academia and industry to study the properties of molecules and materials.
     

  5. Gaussian: Gaussian is a commercial quantum chemistry package that is widely used by researchers in academia and industry. It is known for its accuracy and efficiency.
     

  6. In addition to these general-purpose computational chemistry tools, there are also a number of open source tools that are specialized for specific tasks, such as:
     

  7. VASP: VASP is a plane-wave pseudopotential code for density functional theory (DFT) calculations. It is widely used by researchers in academia and industry to study the properties of solids and materials.
     

  8. FHI-aims: FHI-aims is another plane-wave pseudopotential code for DFT calculations. It is known for its accuracy and efficiency, and it is widely used by researchers in academia to study the properties of solids and materials.
     

  9. Quantum ESPRESSO: Quantum ESPRESSO is a plane-wave pseudopotential code for DFT calculations. It is widely used by researchers in academia and industry to study the properties of solids and materials.
     

  10. LAMMPS: LAMMPS is a molecular dynamics simulation package that is widely used by researchers in academia and industry to study the dynamics and properties of molecules and materials.
     

  11. GROMACS: GROMACS is another molecular dynamics simulation package that is widely used by researchers in academia and industry to study the dynamics and properties of molecules and materials.

 

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COMPUTATIONAL CHEMISTRY - EXPLAINED

​

Computational chemistry is the use of computers to study the structure and properties of molecules and materials. It is a powerful tool that can be used to solve a wide range of problems in chemistry, including:
 

  • Predicting the properties of new molecules

  • Understanding the mechanisms of chemical reactions

  • Designing new catalysts and materials
     

Computational chemistry is based on the principles of quantum mechanics, which describe the behavior of electrons and molecules. Quantum mechanical calculations can be very complex, but computers can be used to solve these equations for relatively large molecules.

 

 

HOW COMPUTATIONAL CHEMISTRY WORKS

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Chemists who use computational methods typically follow these steps:
 

  1. Choose a software package. There are many different computational chemistry software packages available, each with its own strengths and weaknesses. The choice of software package will depend on the specific problem that the chemist is trying to solve.
     

  2. Build a model of the system. The chemist needs to build a model of the system that they are interested in studying. This may involve creating a 3D structure of the molecule or material, and specifying the types of atoms and their interactions.
     

  3. Run the calculation. The chemist then runs the calculation on the computer. This may take hours or even days for complex systems.
     

  4. Analyze the results. Once the calculation is complete, the chemist needs to analyze the results. This may involve looking at the structure of the molecule, the properties of the material, or the mechanism of a chemical reaction.

 

Computational chemistry is a powerful tool that can be used to solve a wide range of problems in chemistry. It is used by chemists in academia and industry to design new materials, catalysts, and drugs.
 

 

Here are some examples of how computational chemistry is used in practice:
 

  • Drug discovery: Computational chemistry can be used to design new drugs by predicting the properties of potential drug candidates and their interactions with biological targets.
     

  • Materials science: Computational chemistry can be used to design new materials with specific properties, such as strength, lightness, or conductivity.
     

  • Catalysis: Computational chemistry can be used to design new catalysts that can speed up chemical reactions.
     

  • Atmospheric chemistry: Computational chemistry can be used to study the chemistry of the atmosphere and to predict the impact of pollutants.
     

Computational chemistry is a rapidly growing field, and new methods and software packages are being developed all the time. As computers become more powerful and algorithms become more efficient, computational chemistry will become even more powerful and versatile.

 

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EVEN MORE CHEMINFORMATICS TOOLS

 

  1. RDKit

    • Description: RDKit is a collection of cheminformatics and machine learning tools for working with chemical structures.

    • Website: RDKit
       

  2. Open Babel

    • Description: Open Babel is an open, collaborative project that provides a chemical toolbox designed to speak the many languages of chemical data.

    • Website: Open Babel
       

  3. Chemistry Development Kit (CDK)

    • Description: CDK is an open-source library for chemoinformatics and bioinformatics. It provides various tools for working with chemical structures and data.

    • Website: CDK
       

  4. Indigo

    • Description: Indigo is a cheminformatics toolkit used for various tasks like molecular layout, substructure search, and rendering chemical structures.

    • Website: Indigo
       

  5. PIKAChU

    • Description: PIKAChU is a tool for pharmacophore-based kinome profiling that can be used for drug discovery and development.

    • Website: PIKAChU
       

  6. KNIME

    • Description: KNIME is an open-source data analytics, reporting, and integration platform that includes various chemistry and bioinformatics extensions.

    • Website: KNIME
       

  7. ChemAxon

    • Description: ChemAxon provides software and services for chemistry, including tools for structure-based design and chemical informatics.

    • Website: ChemAxon
       

  8. ChemmineR

    • Description: ChemmineR is an R package for cheminformatics, offering a wide range of functions for chemical compound analysis.

    • Website: ChemmineR
       

  9. Enalos

    • Description: Enalos is a suite of cheminformatics and computational toxicology tools that help in predicting chemical properties.

    • Website: Enalos
       

  10. Molecular Operating Environment (MOE)

    • Description: MOE is a comprehensive software platform for molecular modeling, simulation, and drug discovery in the life sciences.

    • Website: MOE
       

  11. Open Force Field Toolkit (OPFFTK)

    • Description: OPFFTK is a toolkit for developing and applying molecular mechanics force fields in molecular simulations.

    • Website: OPFFTK
       

  12. ChemoPy

    • Description: ChemoPy is a Python library for chemoinformatics and machine learning applied to chemistry-related tasks.

    • Website: ChemoPy
       

  13. PubChemPy

    • Description: PubChemPy is a Python library for accessing PubChem, a database of chemical compounds maintained by the NCBI.

    • Website: PubChemPy
       

  14. ChemSpiPy

    • Description: ChemSpiPy is a Python library for accessing the ChemSpider database, which contains information about chemical compounds.

    • Website: ChemSpiPy
       

  15. CIRpy

    • Description: CIRpy is a Python library for generating Chemical Identifier Resolver (CIR) numbers for chemical compounds.

    • Website: CIRpy
       

  16. Beaker

    • Description: Beaker is an open-source cheminformatics toolkit designed for working with molecular data.

    • Website: Beaker
       

  17. Chemminetools

    • Description: Chemminetools is a collection of tools and utilities for cheminformatics and compound management.

    • Website: Chemminetools
       

  18. ambit

    • Description: AMBIT is a cheminformatics and toxicology toolset for managing chemical information and predicting toxicity.

    • Website: ambit
       

  19. OpenChem

    • Description: OpenChem is an open-source deep learning framework for computational chemistry and drug discovery.

    • Website: OpenChem
       

  20. DGL-LifeSci

    • Description: DGL-LifeSci is a library for deep learning in life sciences, including cheminformatics and bioinformatics.

    • Website: DGL-LifeSci
       

  21. chainer-chemistry

    • Description: Chainer Chemistry is a deep learning library for chemistry and drug discovery based on the Chainer framework.

    • Website: chainer-chemistry
       

  22. pytorch-geometric

    • Description: PyTorch Geometric is a library for deep learning on irregular structured data, such as molecular graphs.

    • Website: pytorch-geometric
       

  23. chemmodlab

    • Description: ChemModLab is a collection of open-source cheminformatics tools and libraries.

    • Website: chemmodlab
       

  24. Summit

    • Description: Summit is a molecular design platform that combines AI-driven drug discovery with experimental chemistry.

    • Website: Summit

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