SlideShare una empresa de Scribd logo

Protein-Ligand Docking

•Descargar como PPT, PDF•
•
B
baoilleach
Tecnología
1 de 43
Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Protein-ligand docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Images from Charaka Goonatilake’s web page, Glen Group, Unilever Centre, Cambridge
Pose vs. binding site ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Drug Discovery Pipeline C. O’Driscoll. http://www.nature.com/horizon/chemicalspace/background/pdf/odyssey.pdf
Computer-aided drug design (CADD) Known ligand(s) No known ligand Known protein structure Unknown protein structure Structure-based drug design (SBDD) Protein-ligand docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],De novo design CADD of no use Need experimental data of some sort
Uses of docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Virtual screening ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Virtual screening AR Leach, VJ Gillet, An Introduction to Cheminformatics
Components of docking software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Final points ,[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
The search space ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ligand conformations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Taxol Images (from left): IUPAC Gold Book “chair, boat, twist”; “Wikipedia “Taxol”; Lakdawala et al, BMC Chem Biol , 2001 , 1 , 2.
 
Search Algorithms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The DOCK algorithm – Rigid docking ,[object Object],[object Object],[object Object],AR Leach, VJ Gillet, An Introduction to Cheminformatics
The DOCK algorithm – Rigid docking ,[object Object],[object Object],[object Object],AR Leach, VJ Gillet, An Introduction to Cheminformatics
Flexible docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Flexible docking using a Genetic Algorithm (GA) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Handling protein conformations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Image of Tyrosine rotamers from CMBI, Univeristy of Nijmegen at http://www.cmbi.kun.nl/mcsis/richardn/explanation.html
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Components of docking software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The perfect scoring function will… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Classes of scoring function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Empirical scoring functions
Böhm’s empirical scoring function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Böhm’s empirical scoring function ,[object Object],[object Object],[object Object],[object Object]
Knowledge-based potentials ,[object Object],[object Object],[object Object],[object Object],[object Object]
Knowledge-based potentials For example, creating the distributions of ligand carbonyl oxygens to protein hydroxyl groups : (imagine the minimum at 3.0Ang)
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Knowledge-based potentials
Alternative scoring strategies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Pose prediction accuracy ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
AR Leach, VJ Gillet, An Introduction to Cheminformatics
Assess performance of a virtual screen ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Ligand Preparation ,[object Object],[object Object],[object Object],[object Object],[object Object],Enol Ketone
Preparing the protein structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Preparing the protein structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Final thoughts ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI Questions?

Recomendados

Protein ligand docking
Protein ligand dockingProtein ligand docking
Protein ligand dockingUshaYadav24
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingRahul B S
 
MOLECULAR DOCKING
MOLECULAR DOCKINGMOLECULAR DOCKING
MOLECULAR DOCKINGSaramita De Chakravarti
 
Homology modelling
Homology modellingHomology modelling
Homology modellingAyesha Choudhury
 
Structure based drug design
Structure based drug designStructure based drug design
Structure based drug designADAM S
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingShrihith.A Ananthram
 
Lecture 4 ligand based drug design
Lecture 4 ligand based drug designLecture 4 ligand based drug design
Lecture 4 ligand based drug designRAJAN ROLTA
 
Computer aided Drug designing (CADD)
Computer aided Drug designing (CADD)Computer aided Drug designing (CADD)
Computer aided Drug designing (CADD)GlaxoSmithKline Pharma GmbH
 

Recomendados

Protein ligand docking
Protein ligand dockingProtein ligand docking
Protein ligand dockingUshaYadav24
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingRahul B S
 
MOLECULAR DOCKING
MOLECULAR DOCKINGMOLECULAR DOCKING
MOLECULAR DOCKINGSaramita De Chakravarti
 
Homology modelling
Homology modellingHomology modelling
Homology modellingAyesha Choudhury
 
Structure based drug design
Structure based drug designStructure based drug design
Structure based drug designADAM S
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingShrihith.A Ananthram
 
Lecture 4 ligand based drug design
Lecture 4 ligand based drug designLecture 4 ligand based drug design
Lecture 4 ligand based drug designRAJAN ROLTA
 
Computer aided Drug designing (CADD)
Computer aided Drug designing (CADD)Computer aided Drug designing (CADD)
Computer aided Drug designing (CADD)GlaxoSmithKline Pharma GmbH
 
Computational Drug Design
Computational Drug DesignComputational Drug Design
Computational Drug Designbaoilleach
 
docking
docking docking
docking prateek kumar
 
Threading modeling methods
Threading modeling methodsThreading modeling methods
Threading modeling methodsratanvishwas
 
In silico drug desigining
In silico drug desiginingIn silico drug desigining
In silico drug desiginingDevesh Shukla
 
Homology Modelling
Homology ModellingHomology Modelling
Homology ModellingMAYANK ,MEHENDIRATTA
 
Homology modeling
Homology modelingHomology modeling
Homology modelingMalla Reddy College of Pharmacy
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingMaakasaikumar
 
molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
 
Protein 3 d structure prediction
Protein 3 d structure predictionProtein 3 d structure prediction
Protein 3 d structure predictionSamvartika Majumdar
 
Ab Initio Protein Structure Prediction
Ab Initio Protein Structure PredictionAb Initio Protein Structure Prediction
Ab Initio Protein Structure PredictionArindam Ghosh
 
Structure based drug designing
Structure based drug designingStructure based drug designing
Structure based drug designingSeenam Iftikhar
 
De novo drug design
De novo drug designDe novo drug design
De novo drug designmojdeh y
 
MOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxMOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxE Poovarasan
 
Basics Of Molecular Docking
Basics Of Molecular DockingBasics Of Molecular Docking
Basics Of Molecular DockingSatarupa Deb
 
De novo drug design
De novo drug designDe novo drug design
De novo drug designPrasanthperceptron
 
Docking Score Functions
Docking Score FunctionsDocking Score Functions
Docking Score FunctionsSAKEEL AHMED
 
Protein-ligand docking
Protein-ligand dockingProtein-ligand docking
Protein-ligand dockingbaoilleach
 
Virtual Screening in Drug Discovery
Virtual Screening in Drug DiscoveryVirtual Screening in Drug Discovery
Virtual Screening in Drug DiscoveryAbhik Seal
 
Protein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modelingProtein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modelingBioinformatics and Computational Biosciences Branch
 
methods for protein structure prediction
methods for protein structure predictionmethods for protein structure prediction
methods for protein structure predictionkaramveer prajapat
 
Molecular docking
Molecular dockingMolecular docking
Molecular dockingpalliyath91
 
Protein docking
Protein dockingProtein docking
Protein dockingSenthil Natesan
 

Más contenido relacionado

La actualidad más candente

Computational Drug Design
Computational Drug DesignComputational Drug Design
Computational Drug Designbaoilleach
 
Threading modeling methods
Threading modeling methodsThreading modeling methods
Threading modeling methodsratanvishwas
 
In silico drug desigining
In silico drug desiginingIn silico drug desigining
In silico drug desiginingDevesh Shukla
 
molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
 
Protein 3 d structure prediction
Protein 3 d structure predictionProtein 3 d structure prediction
Protein 3 d structure predictionSamvartika Majumdar
 
Ab Initio Protein Structure Prediction
Ab Initio Protein Structure PredictionAb Initio Protein Structure Prediction
Ab Initio Protein Structure PredictionArindam Ghosh
 
Structure based drug designing
Structure based drug designingStructure based drug designing
Structure based drug designingSeenam Iftikhar
 
De novo drug design
De novo drug designDe novo drug design
De novo drug designmojdeh y
 
MOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxMOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxE Poovarasan
 
Basics Of Molecular Docking
Basics Of Molecular DockingBasics Of Molecular Docking
Basics Of Molecular DockingSatarupa Deb
 
Docking Score Functions
Docking Score FunctionsDocking Score Functions
Docking Score FunctionsSAKEEL AHMED
 
Protein-ligand docking
Protein-ligand dockingProtein-ligand docking
Protein-ligand dockingbaoilleach
 
Virtual Screening in Drug Discovery
Virtual Screening in Drug DiscoveryVirtual Screening in Drug Discovery
Virtual Screening in Drug DiscoveryAbhik Seal
 
methods for protein structure prediction
methods for protein structure predictionmethods for protein structure prediction
methods for protein structure predictionkaramveer prajapat
 

La actualidad más candente (20)

Computational Drug Design
Computational Drug DesignComputational Drug Design
Computational Drug Design
 
docking
docking docking
docking
 
Threading modeling methods
Threading modeling methodsThreading modeling methods
Threading modeling methods
 
In silico drug desigining
In silico drug desiginingIn silico drug desigining
In silico drug desigining
 
Homology Modelling
Homology ModellingHomology Modelling
Homology Modelling
 
Homology modeling
Homology modelingHomology modeling
Homology modeling
 
Molecular docking
Molecular dockingMolecular docking
Molecular docking
 
molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...molecular docking its types and de novo drug design and application and softw...
molecular docking its types and de novo drug design and application and softw...
 
Protein 3 d structure prediction
Protein 3 d structure predictionProtein 3 d structure prediction
Protein 3 d structure prediction
 
Ab Initio Protein Structure Prediction
Ab Initio Protein Structure PredictionAb Initio Protein Structure Prediction
Ab Initio Protein Structure Prediction
 
Structure based drug designing
Structure based drug designingStructure based drug designing
Structure based drug designing
 
De novo drug design
De novo drug designDe novo drug design
De novo drug design
 
MOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxMOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptx
 
Basics Of Molecular Docking
Basics Of Molecular DockingBasics Of Molecular Docking
Basics Of Molecular Docking
 
De novo drug design
De novo drug designDe novo drug design
De novo drug design
 
Docking Score Functions
Docking Score FunctionsDocking Score Functions
Docking Score Functions
 
Protein-ligand docking
Protein-ligand dockingProtein-ligand docking
Protein-ligand docking
 
Virtual Screening in Drug Discovery
Virtual Screening in Drug DiscoveryVirtual Screening in Drug Discovery
Virtual Screening in Drug Discovery
 
Protein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modelingProtein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modeling
 
methods for protein structure prediction
methods for protein structure predictionmethods for protein structure prediction
methods for protein structure prediction
 

Destacado

Molecular docking
Molecular dockingMolecular docking
Molecular dockingpalliyath91
 
molecular docking
molecular dockingmolecular docking
molecular dockingKOUSHIK DEB
 
Molecular docking and_virtual_screening
Molecular docking and_virtual_screeningMolecular docking and_virtual_screening
Molecular docking and_virtual_screeningFlorent Barbault
 
Interaction fingerprint: 1D representation of 3D protein-ligand complexes
Interaction fingerprint: 1D representation of 3D protein-ligand complexesInteraction fingerprint: 1D representation of 3D protein-ligand complexes
Interaction fingerprint: 1D representation of 3D protein-ligand complexesVladimir Chupakhin
 
Protein ligand interaction.
Protein ligand interaction.Protein ligand interaction.
Protein ligand interaction.Rachana Tiwari
 
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS santosh Kumbhar
 
9.protein ligand interactions2
9.protein ligand interactions29.protein ligand interactions2
9.protein ligand interactions2Abhijeet Kadam
 
Computer aided drug designing (CADD)
Computer aided drug designing (CADD)Computer aided drug designing (CADD)
Computer aided drug designing (CADD)Aakshay Subramaniam
 
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERY
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERYSTRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERY
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERYTHILAKAR MANI
 
AutoDock_vina_japanese_ver.3.0
AutoDock_vina_japanese_ver.3.0AutoDock_vina_japanese_ver.3.0
AutoDock_vina_japanese_ver.3.0Satoshi Kume
 
Drug discovery Using Bioinformatic
Drug discovery Using BioinformaticDrug discovery Using Bioinformatic
Drug discovery Using BioinformaticSuhad Jihad
 
8.protein ligand interactions
8.protein ligand interactions8.protein ligand interactions
8.protein ligand interactionsAbhijeet Kadam
 
Homology modeling and molecular docking
Homology modeling and molecular dockingHomology modeling and molecular docking
Homology modeling and molecular dockingRangika Munaweera
 
Computer Aided Drug Design and Discovery : An Overview (2006)
Computer Aided Drug Design and Discovery : An Overview (2006)Computer Aided Drug Design and Discovery : An Overview (2006)
Computer Aided Drug Design and Discovery : An Overview (2006)Girinath Pillai
 
Computer aided drug designing
Computer aided drug designingComputer aided drug designing
Computer aided drug designingMuhammed sadiq
 
protein sturcture prediction and molecular modelling
protein sturcture prediction and molecular modellingprotein sturcture prediction and molecular modelling
protein sturcture prediction and molecular modellingDileep Paruchuru
 

Destacado (20)

Molecular docking
Molecular dockingMolecular docking
Molecular docking
 
Protein docking
Protein dockingProtein docking
Protein docking
 
molecular docking
molecular dockingmolecular docking
molecular docking
 
Molecular docking and_virtual_screening
Molecular docking and_virtual_screeningMolecular docking and_virtual_screening
Molecular docking and_virtual_screening
 
Interaction fingerprint: 1D representation of 3D protein-ligand complexes
Interaction fingerprint: 1D representation of 3D protein-ligand complexesInteraction fingerprint: 1D representation of 3D protein-ligand complexes
Interaction fingerprint: 1D representation of 3D protein-ligand complexes
 
Protein ligand interaction.
Protein ligand interaction.Protein ligand interaction.
Protein ligand interaction.
 
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS
MOLECULAR DOCKING AND RELATED DRUG DESIGN ACHIEVEMENTS
 
9.protein ligand interactions2
9.protein ligand interactions29.protein ligand interactions2
9.protein ligand interactions2
 
CADD Lecture
CADD LectureCADD Lecture
CADD Lecture
 
Computer aided drug designing (CADD)
Computer aided drug designing (CADD)Computer aided drug designing (CADD)
Computer aided drug designing (CADD)
 
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERY
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERYSTRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERY
STRUCTURE BASED DRUG DESIGN - MOLECULAR MODELLING AND DRUG DISCOVERY
 
Computer Aided Drug Design ppt
Computer Aided Drug Design pptComputer Aided Drug Design ppt
Computer Aided Drug Design ppt
 
AutoDock_vina_japanese_ver.3.0
AutoDock_vina_japanese_ver.3.0AutoDock_vina_japanese_ver.3.0
AutoDock_vina_japanese_ver.3.0
 
Machine learning in computational docking
Machine learning in computational dockingMachine learning in computational docking
Machine learning in computational docking
 
Drug discovery Using Bioinformatic
Drug discovery Using BioinformaticDrug discovery Using Bioinformatic
Drug discovery Using Bioinformatic
 
8.protein ligand interactions
8.protein ligand interactions8.protein ligand interactions
8.protein ligand interactions
 
Homology modeling and molecular docking
Homology modeling and molecular dockingHomology modeling and molecular docking
Homology modeling and molecular docking
 
Computer Aided Drug Design and Discovery : An Overview (2006)
Computer Aided Drug Design and Discovery : An Overview (2006)Computer Aided Drug Design and Discovery : An Overview (2006)
Computer Aided Drug Design and Discovery : An Overview (2006)
 
Computer aided drug designing
Computer aided drug designingComputer aided drug designing
Computer aided drug designing
 
protein sturcture prediction and molecular modelling
protein sturcture prediction and molecular modellingprotein sturcture prediction and molecular modelling
protein sturcture prediction and molecular modelling
 

Similar a Protein-Ligand Docking

43_EMIJ-06-00212.pdf
43_EMIJ-06-00212.pdf43_EMIJ-06-00212.pdf
43_EMIJ-06-00212.pdfUmeshYadava1
 
P. Joshi SBDD and docking.ppt
P. Joshi SBDD and docking.pptP. Joshi SBDD and docking.ppt
P. Joshi SBDD and docking.pptpranalpatilPranal
 
Structure based drug design- kiranmayi
Structure based drug design- kiranmayiStructure based drug design- kiranmayi
Structure based drug design- kiranmayiKiranmayiKnv
 
COMPUTER AIDED DRUG DESIGN.pptx
COMPUTER AIDED DRUG DESIGN.pptxCOMPUTER AIDED DRUG DESIGN.pptx
COMPUTER AIDED DRUG DESIGN.pptxSumitMaji13
 
molecular docking screnning. pptx
molecular docking screnning. pptxmolecular docking screnning. pptx
molecular docking screnning. pptxPraveen kumar S
 
Docking techniques
Docking techniquesDocking techniques
Docking techniquesDevika Rana
 
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERY
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERYMOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERY
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERYRajratan Thorat
 
Target oriented generic fingerprint-based molecular representation
Target oriented generic fingerprint-based molecular representationTarget oriented generic fingerprint-based molecular representation
Target oriented generic fingerprint-based molecular representationcsandit
 
DENOVO DRUG DESIGN AS PER PCI SYLLABUS
DENOVO DRUG DESIGN AS PER PCI SYLLABUSDENOVO DRUG DESIGN AS PER PCI SYLLABUS
DENOVO DRUG DESIGN AS PER PCI SYLLABUSShikha Popali
 
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARM
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARMDENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARM
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARMShikha Popali
 
Bioinformatics-2016-Basu-i262-70
Bioinformatics-2016-Basu-i262-70Bioinformatics-2016-Basu-i262-70
Bioinformatics-2016-Basu-i262-70sankar basu
 
Structural Bioinformatics.pdf
Structural Bioinformatics.pdfStructural Bioinformatics.pdf
Structural Bioinformatics.pdfRahmatEkoSanjaya1
 

Similar a Protein-Ligand Docking (20)

43_EMIJ-06-00212.pdf
43_EMIJ-06-00212.pdf43_EMIJ-06-00212.pdf
43_EMIJ-06-00212.pdf
 
P. Joshi SBDD and docking.ppt
P. Joshi SBDD and docking.pptP. Joshi SBDD and docking.ppt
P. Joshi SBDD and docking.ppt
 
Structure based drug design- kiranmayi
Structure based drug design- kiranmayiStructure based drug design- kiranmayi
Structure based drug design- kiranmayi
 
Molecular docking
Molecular dockingMolecular docking
Molecular docking
 
COMPUTER AIDED DRUG DESIGN.pptx
COMPUTER AIDED DRUG DESIGN.pptxCOMPUTER AIDED DRUG DESIGN.pptx
COMPUTER AIDED DRUG DESIGN.pptx
 
molecular docking screnning. pptx
molecular docking screnning. pptxmolecular docking screnning. pptx
molecular docking screnning. pptx
 
Docking techniques
Docking techniquesDocking techniques
Docking techniques
 
CADD
CADDCADD
CADD
 
Denovo Drug Design
Denovo Drug DesignDenovo Drug Design
Denovo Drug Design
 
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERY
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERYMOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERY
MOLECULAR DOCKING PRINCIPAL OF DRUG DISCOVERY
 
Target oriented generic fingerprint-based molecular representation
Target oriented generic fingerprint-based molecular representationTarget oriented generic fingerprint-based molecular representation
Target oriented generic fingerprint-based molecular representation
 
Denovo
DenovoDenovo
Denovo
 
Dock Sem
Dock SemDock Sem
Dock Sem
 
DENOVO DRUG DESIGN AS PER PCI SYLLABUS
DENOVO DRUG DESIGN AS PER PCI SYLLABUSDENOVO DRUG DESIGN AS PER PCI SYLLABUS
DENOVO DRUG DESIGN AS PER PCI SYLLABUS
 
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARM
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARMDENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARM
DENOVO DRUG DESIGN AS PER PCI SYLLABUS M.PHARM
 
Autodock review ppt
Autodock review pptAutodock review ppt
Autodock review ppt
 
Virtual sreening
Virtual sreeningVirtual sreening
Virtual sreening
 
Bioinformatics-2016-Basu-i262-70
Bioinformatics-2016-Basu-i262-70Bioinformatics-2016-Basu-i262-70
Bioinformatics-2016-Basu-i262-70
 
MOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptxMOLECULAR DOCKING.pptx
MOLECULAR DOCKING.pptx
 
Structural Bioinformatics.pdf
Structural Bioinformatics.pdfStructural Bioinformatics.pdf
Structural Bioinformatics.pdf
 

Más de baoilleach

We need to talk about Kekulization, Aromaticity and SMILES
We need to talk about Kekulization, Aromaticity and SMILESWe need to talk about Kekulization, Aromaticity and SMILES
We need to talk about Kekulization, Aromaticity and SMILESbaoilleach
 
Open Babel project overview
Open Babel project overviewOpen Babel project overview
Open Babel project overviewbaoilleach
 
So I have an SD File... What do I do next?
So I have an SD File... What do I do next?So I have an SD File... What do I do next?
So I have an SD File... What do I do next?baoilleach
 
Chemistrify the Web
Chemistrify the WebChemistrify the Web
Chemistrify the Webbaoilleach
 
Universal Smiles: Finally a canonical SMILES string
Universal Smiles: Finally a canonical SMILES stringUniversal Smiles: Finally a canonical SMILES string
Universal Smiles: Finally a canonical SMILES stringbaoilleach
 
What's New and Cooking in Open Babel 2.3.2
What's New and Cooking in Open Babel 2.3.2What's New and Cooking in Open Babel 2.3.2
What's New and Cooking in Open Babel 2.3.2baoilleach
 
Intro to Open Babel
Intro to Open BabelIntro to Open Babel
Intro to Open Babelbaoilleach
 
Cheminformatics
CheminformaticsCheminformatics
Cheminformaticsbaoilleach
 
Making the most of a QM calculation
Making the most of a QM calculationMaking the most of a QM calculation
Making the most of a QM calculationbaoilleach
 
Data Analysis in QSAR
Data Analysis in QSARData Analysis in QSAR
Data Analysis in QSARbaoilleach
 
Large-scale computational design and selection of polymers for solar cells
Large-scale computational design and selection of polymers for solar cellsLarge-scale computational design and selection of polymers for solar cells
Large-scale computational design and selection of polymers for solar cellsbaoilleach
 
My Open Access papers
My Open Access papersMy Open Access papers
My Open Access papersbaoilleach
 
Improving the quality of chemical databases with community-developed tools (a...
Improving the quality of chemical databases with community-developed tools (a...Improving the quality of chemical databases with community-developed tools (a...
Improving the quality of chemical databases with community-developed tools (a...baoilleach
 
De novo design of molecular wires with optimal properties for solar energy co...
De novo design of molecular wires with optimal properties for solar energy co...De novo design of molecular wires with optimal properties for solar energy co...
De novo design of molecular wires with optimal properties for solar energy co...baoilleach
 
Cinfony - Bring cheminformatics toolkits into tune
Cinfony - Bring cheminformatics toolkits into tuneCinfony - Bring cheminformatics toolkits into tune
Cinfony - Bring cheminformatics toolkits into tunebaoilleach
 
Density functional theory calculations on Ruthenium polypyridyl complexes inc...
Density functional theory calculations on Ruthenium polypyridyl complexes inc...Density functional theory calculations on Ruthenium polypyridyl complexes inc...
Density functional theory calculations on Ruthenium polypyridyl complexes inc...baoilleach
 
Application of Density Functional Theory to Scanning Tunneling Microscopy
Application of Density Functional Theory to Scanning Tunneling MicroscopyApplication of Density Functional Theory to Scanning Tunneling Microscopy
Application of Density Functional Theory to Scanning Tunneling Microscopybaoilleach
 
Towards Practical Molecular Devices
Towards Practical Molecular DevicesTowards Practical Molecular Devices
Towards Practical Molecular Devicesbaoilleach
 
Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...baoilleach
 
Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...baoilleach
 

Más de baoilleach (20)

We need to talk about Kekulization, Aromaticity and SMILES
We need to talk about Kekulization, Aromaticity and SMILESWe need to talk about Kekulization, Aromaticity and SMILES
We need to talk about Kekulization, Aromaticity and SMILES
 
Open Babel project overview
Open Babel project overviewOpen Babel project overview
Open Babel project overview
 
So I have an SD File... What do I do next?
So I have an SD File... What do I do next?So I have an SD File... What do I do next?
So I have an SD File... What do I do next?
 
Chemistrify the Web
Chemistrify the WebChemistrify the Web
Chemistrify the Web
 
Universal Smiles: Finally a canonical SMILES string
Universal Smiles: Finally a canonical SMILES stringUniversal Smiles: Finally a canonical SMILES string
Universal Smiles: Finally a canonical SMILES string
 
What's New and Cooking in Open Babel 2.3.2
What's New and Cooking in Open Babel 2.3.2What's New and Cooking in Open Babel 2.3.2
What's New and Cooking in Open Babel 2.3.2
 
Intro to Open Babel
Intro to Open BabelIntro to Open Babel
Intro to Open Babel
 
Cheminformatics
CheminformaticsCheminformatics
Cheminformatics
 
Making the most of a QM calculation
Making the most of a QM calculationMaking the most of a QM calculation
Making the most of a QM calculation
 
Data Analysis in QSAR
Data Analysis in QSARData Analysis in QSAR
Data Analysis in QSAR
 
Large-scale computational design and selection of polymers for solar cells
Large-scale computational design and selection of polymers for solar cellsLarge-scale computational design and selection of polymers for solar cells
Large-scale computational design and selection of polymers for solar cells
 
My Open Access papers
My Open Access papersMy Open Access papers
My Open Access papers
 
Improving the quality of chemical databases with community-developed tools (a...
Improving the quality of chemical databases with community-developed tools (a...Improving the quality of chemical databases with community-developed tools (a...
Improving the quality of chemical databases with community-developed tools (a...
 
De novo design of molecular wires with optimal properties for solar energy co...
De novo design of molecular wires with optimal properties for solar energy co...De novo design of molecular wires with optimal properties for solar energy co...
De novo design of molecular wires with optimal properties for solar energy co...
 
Cinfony - Bring cheminformatics toolkits into tune
Cinfony - Bring cheminformatics toolkits into tuneCinfony - Bring cheminformatics toolkits into tune
Cinfony - Bring cheminformatics toolkits into tune
 
Density functional theory calculations on Ruthenium polypyridyl complexes inc...
Density functional theory calculations on Ruthenium polypyridyl complexes inc...Density functional theory calculations on Ruthenium polypyridyl complexes inc...
Density functional theory calculations on Ruthenium polypyridyl complexes inc...
 
Application of Density Functional Theory to Scanning Tunneling Microscopy
Application of Density Functional Theory to Scanning Tunneling MicroscopyApplication of Density Functional Theory to Scanning Tunneling Microscopy
Application of Density Functional Theory to Scanning Tunneling Microscopy
 
Towards Practical Molecular Devices
Towards Practical Molecular DevicesTowards Practical Molecular Devices
Towards Practical Molecular Devices
 
Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...
 
Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...Why multiple scoring functions can improve docking performance - Testing hypo...
Why multiple scoring functions can improve docking performance - Testing hypo...
 

Último

Corporate and higher education May webinar.pptx
Corporate and higher education May webinar.pptxCorporate and higher education May webinar.pptx
Corporate and higher education May webinar.pptxRustici Software
 
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMECloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMESafe Software
 
Vector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptxVector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptxRemote DBA Services
 
MS Copilot expands with MS Graph connectors
MS Copilot expands with MS Graph connectorsMS Copilot expands with MS Graph connectors
MS Copilot expands with MS Graph connectorsNanddeep Nachan
 
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...apidays
 
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024Victor Rentea
 
Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood
Polkadot JAM Slides - Token2049 - By Dr. Gavin WoodPolkadot JAM Slides - Token2049 - By Dr. Gavin Wood
Polkadot JAM Slides - Token2049 - By Dr. Gavin WoodJuan lago vázquez
 
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdf
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdfRising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdf
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdfOrbitshub
 
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingRepurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingEdi Saputra
 
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWEREMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWERMadyBayot
 
Architecting Cloud Native Applications
Architecting Cloud Native ApplicationsArchitecting Cloud Native Applications
Architecting Cloud Native ApplicationsWSO2
 
[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdf[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdfSandro Moreira
 
AWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of TerraformAWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of TerraformAndrey Devyatkin
 
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemkeProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemkeProduct Anonymous
 
Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024Victor Rentea
 
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...apidays
 
Platformless Horizons for Digital Adaptability
Platformless Horizons for Digital AdaptabilityPlatformless Horizons for Digital Adaptability
Platformless Horizons for Digital AdaptabilityWSO2
 
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobe
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, AdobeApidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobe
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobeapidays
 
How to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerHow to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerThousandEyes
 
TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data DiscoveryTrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data DiscoveryTrustArc
 

Último (20)

Corporate and higher education May webinar.pptx
Corporate and higher education May webinar.pptxCorporate and higher education May webinar.pptx
Corporate and higher education May webinar.pptx
 
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMECloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
 
Vector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptxVector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptx
 
MS Copilot expands with MS Graph connectors
MS Copilot expands with MS Graph connectorsMS Copilot expands with MS Graph connectors
MS Copilot expands with MS Graph connectors
 
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...
Apidays New York 2024 - Accelerating FinTech Innovation by Vasa Krishnan, Fin...
 
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024
Modular Monolith - a Practical Alternative to Microservices @ Devoxx UK 2024
 
Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood
Polkadot JAM Slides - Token2049 - By Dr. Gavin WoodPolkadot JAM Slides - Token2049 - By Dr. Gavin Wood
Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood
 
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdf
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdfRising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdf
Rising Above_ Dubai Floods and the Fortitude of Dubai International Airport.pdf
 
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingRepurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
 
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWEREMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER
EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER
 
Architecting Cloud Native Applications
Architecting Cloud Native ApplicationsArchitecting Cloud Native Applications
Architecting Cloud Native Applications
 
[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdf[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdf
 
AWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of TerraformAWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of Terraform
 
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemkeProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
 
Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024
 
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
 
Platformless Horizons for Digital Adaptability
Platformless Horizons for Digital AdaptabilityPlatformless Horizons for Digital Adaptability
Platformless Horizons for Digital Adaptability
 
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobe
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, AdobeApidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobe
Apidays New York 2024 - Scaling API-first by Ian Reasor and Radu Cotescu, Adobe
 
How to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerHow to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected Worker
 
TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data DiscoveryTrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
 

Protein-Ligand Docking

  • 1. Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI
  • 2.
  • 3.
  • 4.
  • 5.
  • 6. Drug Discovery Pipeline C. O’Driscoll. http://www.nature.com/horizon/chemicalspace/background/pdf/odyssey.pdf
  • 7.
  • 8.
  • 9.
  • 10. Virtual screening AR Leach, VJ Gillet, An Introduction to Cheminformatics
  • 11.
  • 12.
  • 13.
  • 14.
  • 15.
  • 16.  
  • 17.
  • 18.
  • 19.
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25.
  • 26.
  • 28.
  • 29.
  • 30.
  • 31. Knowledge-based potentials For example, creating the distributions of ligand carbonyl oxygens to protein hydroxyl groups : (imagine the minimum at 3.0Ang)
  • 32.
  • 33.
  • 34.
  • 35.
  • 36. AR Leach, VJ Gillet, An Introduction to Cheminformatics
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
  • 42.
  • 43. Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI Questions?

Notas del editor

  1. Images from Wikipedia entry for Taxol
  2. Image from Wikipedia “12-6-Lennard-Jones-Potential.png”
  3. Expected = 5% of 10 = 0.5 actives Enrichment = 2 / 0.5 = 4.0