chemoinformatics and bioinformatics

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