- MED-SuMo
- CAVER
- FINDSITE
- sc-PDB
- Pocketome
- PocketAnnotatedatabase
- 3DLigandSite
- metaPocket
- PocketAnnotate

Examples of Binding Site Prediction Softwares (CADD)


Softwares that use computational methods for the prediction of binding sites. Binding sites are pockets of protein that can be used to bind drugs and this is an important step in the drug design process which can save a lot of resources.


University of Illinois at Urbana-Champaign

CADD can be used in the following areas of drug design:

- Molecular Modeling 
- Binding Free Energy Estimation Software 
- Binding Site Prediction Software
- Homology Modeling
- QSAR Software
- ADME Toxicity Software
- Ligand Design Software 
- Draw Tools
- Databases
- Docking Software
- Screening Software
- Target Prediction Software

CADD Concepts


https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3058-0

BMC Bioinformatics

A gene, nucleic acid, or protein that may potentially combat a specific disease.

Target


Molecular modeling refers to all the theoretical and computational methods used to model the behavior of molecules. Calculation that are relatively simple can be performed by hand, but inevitably computers are required in the molecular modeling of a reasonably sized system.

  Molecular modeling is used to reduce time and cost in the early stages of drug discovery.


Molecular modeling softwares (CADD)


Softwares that are used to calculate binding affinities of compounds to their primary target. This would allow concentrating efforts in more promising compounds thereby speeding up the drug development process.


Binding Free Energy Estimation Softwares (CADD)

Binding Site Prediction Softwares (CADD)


Homology modeling softwares use computational methods for protein structure prediction from its amino acid sequences.


Homology Modeling  (CADD)


These softwares are used to predict mathematical models which is used to provide insight into the chemical and biological properties of novel compounds.


QSAR softwares (CADD)

Softwares that predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs. 


ADME Toxicity Softwares (CADD)


Softwares that aid with the process of ligand-based drug design  which  relies on the knowledge of molecules that bind to the biological target.


Ligand Design Software (CADD)

Draw tools allow researchers to sketch chemical compounds, structures, and reactions.

Draw Tools (CADD)

Chemical databases can speed up the computational methods to build a  hypothesis for the discovery and design of a new drug thereby reducing time and cost. There are large amounts of chemical information available as public chemical databases that researchers can make use of.


Databases (CADD)

Docking is used to predict the preferred orientation of a molecule when it binds to another to form a stable complex. Docking softwares aid drug design by predicting intermolecular frameworks between proteins and proteins or proteins and small molecules.


Docking Softwares (CADD)


These softwares make use of virtual screening tools to predict structures that are most likely to bind to a drug target.


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