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Chemoinformatics And Bioinformatics. Cédric Notredame. Molecular Biology. Bioinformatics. Chemoinformatics. Chemistry. Bioinformatics and Chemoinformatics. Scale. Bioinformatics. Chemoinformatics. Sequences ----------(Structures)-----------Ligands/Lead. Genes Genomes. Drugs. - PowerPoint PPT Presentation
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Cédric Notredame (20/04/23)
ChemoinformaticsAnd
BioinformaticsCédric Notredame
Molecular Biology
Bioinformatics
Chemoinformatics
Chemistry
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences ----------(Structures)-----------Ligands/Lead
GenesGenomes
Drugs
Scale
Proteins
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences -----------(Structures)-----------Ligands
Chain EachAtom
AGCTGTCGAGGGATAGGACATATACATAAATTAATATAAT
Describing the DATA
StringsSMILES, Sybyl,
Matrices…
Structure Descriptors
ChainAtom
3D-Structure
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences -------------(Structures)---------------Ligands
ChainEachAtom
AGCTGTCGAGGGATAGGACATATACATAAATTAATATAAT
Storing the DATA
Strings
SMILES, Sybyl, Matrices,
descriptors
ChainAtom
3D-Structure
Sequence Chemical Structure
Coordinates
PDBGenBank: GenomesGenpep/NR: proteinsSwissProt
CAPLUSREGISTRY…
Cédric Notredame (20/04/23)
Related TechniquesDatabases
Bioinformatics:NCBI/EBI
ChemoinformaticsCAS/Beilstein/MDL
Finding the right Databaseis NOT an issue as most dataare public.
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences -----------(Structures)-----------Ligands
Similarity Descriptor
Comparing the DATA
Evolutionary model Descriptor Similarity
Fold
3D-Model
Dynamic Programming Structure/StructureComparison
Backtracking Algorithm
BLAST LSQmanDALISAP
CACTUS(Cactus.nci.nih.gov)
Cédric Notredame (20/04/23)
Related TechniquesSearching Databases
Bioinformatics:Dynamic Programming
ChemoinformaticsBacktracking
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences -----------(Structures)-----------Ligands
MSA Descriptor
Building Models
MultipleSequence Alignments
ClustalW, TCoffee
Descriptor Computation
Fold
3D-Model
Classifications
DALISCOPCAT
Cédric Notredame (20/04/23)
Related TechniquesProfiles
Bioinformatics: Chemoinformatics
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
ChemoinformaticsBioinformatics
Sequences -----------(Structures)-----------Ligands
Function Descriptor
Predicting Properties
Multiple Comparisons QSAR
Binding
Docking/Mecanisms
StructurePhylogeny
Molecular DynamicDocking PredictionsFunction
Relate descriptors to
Activity/Toxicity
Profiles Pfam
Cédric Notredame (20/04/23)
Related TechniquesProfiles and Descriptors
Bioinformatics: Chemoinformatics
Database Search With a Profile
Pharmacophore
Database Search With a Profile
Cédric Notredame (20/04/23)
Bioinformatics/ Chemoinformatics
Each One in its Niche
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
The Questions Bioinformatics:
TargetChemoinformatics
Lead
Target
Site
Compound Database
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
The Questions
Evolutionary Trace
Chemical Modelling
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
The Questions Bioinformatics:
FunctionChemoinformatics
QSAR
Comparative Genomics
Function
Quantitative Structure-Activity
Relationship
Activity/Toxicity
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
The Questions Bioinformatics:
TargetChemoinformatics
Lead
Comparative GenomicsMolecular Dynamic
Docking
2D/3D QSARMolecular Dynamic
In Silico Screening
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
The Algorithms
Bioinformatics: Target
ChemoinformaticsLead
Dynamic Programming
Backtrace
Graph Theory
Neural Networks
Genetic Algorithms
Hidden Markov Models
Cédric Notredame (20/04/23)
Bioinformatics/ Chemoinformatics
Where Do They Meet
Cédric Notredame (20/04/23)
Homology based SAR predictions
Cédric Notredame (20/04/23)
• SAR Matrices contain affinity Data
Homology based SAR predictions
Cédric Notredame (20/04/23)
• Targets can be clustered from the SAR Data
Homology based SAR predictions
Cédric Notredame (20/04/23)
• Targets can be clustered using similarity
Homology based SAR predictions
Cédric Notredame (20/04/23)
• Sequence Clustering Can be done using Key positions
Homology based SAR predictions
Cédric Notredame (20/04/23)
• Sequence Clustering Can be done using Key positions
Homology based SAR predictions
Cédric Notredame (20/04/23)
• Does it Work ???
– Clustering Based on Active Site Residues
Homology based SAR predictions
Cédric Notredame (20/04/23)
Homology based SAR predictions
–Pairs of Comparable Kinases
Cédric Notredame (20/04/23)
Bioinformatics/ Chemoinformatics
Main Differences ?
Cédric Notredame (20/04/23)
Bioinformatics and Chemoinformatics
Bioinformatics: Chemoinformatics
Macro-molecules Small Molecules
Evolutionary Signal Chemical Modelling
