Chemical Space
Chemical space refers to the vast and multidimensional space that encompasses all possible chemical compounds or molecules. It represents the diversity and variability of chemical structures that can exist based on different combinations of atoms, bonds, and functional groups.
this seminar was all about the structure library creation using varios techniquse and free tools, most of the concepts the author tolds were considerably hard to undeerstand but i did understand somw basic topics of creating a structur library.
Purpose
The main purpose of structure library genderation is to boost up novel design of new compounds.
The term "epigenetic target profile" refers to the collection of molecular targets or proteins that are involved in epigenetic processes and can be modulated or influenced by small molecules or drugs. Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype that do not involve changes in the DNA sequence itself. Epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNA molecules, play a crucial role in regulating gene expression and cellular function.
Free tool
i did't understand completely
- www.difacquim.com/d-tools/ (opens in a new tab) (last time i check it was not working!)
- natural product library
Resent research advances
- To identification and developmemnt of compounds based on their epigenetic center.
- can also be used for the analysis of natural food and compounds in food.
- design of library and several automation.
as per the guide in the seminar...
Chemical Space
'An M-dimensional Cartesian space in which compounds are located by a set of M Physiochemical and/or Cheminformatics descriptors.'
Chemical Space : Chemical space is a concept in cheminformatics referring to the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. It contains millions of compounds which are readily accessible and available to researchers. It is a library used in the method of molecular docking.
| Chemical Compounds types | ID | Physiochemical propeties | topological descriptio | Molecular Fragments | Similara vusual based shapes |
|---|---|---|---|---|---|
| Approved Drugs | M1 | ||||
| Natural Products | M2 | ||||
| food Chemical | M3 | ||||
| Virtual compounds | M4 | ||||
| Synthesizable | M5 | ||||
| Organometallic Compounds | M6 | ||||
| Peptides | M7 | ||||
| Others | Mn | ... | ... | ... | ... |
Descriptiors
Descriptors are the basic property that a chemical holds which can be 1D, 2D, 3D, physical, chemical like fingerprints,substructures,topology surface area, electronic configrution of the compounds etc...
Descriptors tools
descriptor tools can be accessed through Rdkit, Pydescriptor (PyMol plugin) ,ChemDes (Web-application), and even SwissADME is also a really good choice.
Gools to study in descriptor study
Nature type of study: organic, metallic, organometaliic, biomolecule, peptide
Number of molecules are also important because the performace is also dependent on the calculation method.
Conceptual Framework of cheminformatics
| Quntum Chemistry | Force Field Based Molecular Modeleling | Cheminformatics | |
|---|---|---|---|
| Molecular Modal | Electron and Nuclei | Atoms and bonds | Graphs and descriptor vectors |
| Inference MEchanism | Deductive >> inductive | Deductive =~ inductive | Deductive < inductive |
Fingerprints
MAP4 is a new molecular fingerprint performing as good as extended connectivity fingerprints such as ECFP4 and MHFP6 on the Riniker and Landrum small molecule benchmark, and as good as the RDkit AP fingerprint on a new peptide sequence similarity benchmarking set for recovering BLAST analogs among scrambled and mutated
MACCS keys are 166-bit 2D structure fingerprints that are commonly used for the measure of molecular similarity.