Chemoinformatics: a Hot Chemoinformatics: a Hot Topic in Distance Topic in Distance Education Education Zarrin Es’haghi Zarrin Es’haghi Department of Chemistry, Faculty of Department of Chemistry, Faculty of Sciences Sciences Payame Noor University, Mashhad, Iran Payame Noor University, Mashhad, Iran Payame Noor University
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Chemoinformatics: a Hot Topic in Chemoinformatics: a Hot Topic in
Distance EducationDistance Education
Zarrin Es’haghiZarrin Es’haghi
Department of Chemistry, Faculty of SciencesDepartment of Chemistry, Faculty of Sciences
Payame Noor University, Mashhad, IranPayame Noor University, Mashhad, Iran
E-Mail: [email protected]: [email protected]
Payame Noor University
Chemoinformatics: a Hot Topic in Chemoinformatics: a Hot Topic in
Distance EducationDistance Education
Zarrin Es’haghiZarrin Es’haghi
Department of Chemistry, Faculty of SciencesDepartment of Chemistry, Faculty of Sciences
Payame Noor University, Mashhad, IranPayame Noor University, Mashhad, Iran
E-Mail: [email protected]: [email protected]
Payame Noor University
3
Chemoinformatics Chem(o)informatics is a generic
term that encompasses the; design, creation, organization, design, creation, organization,
management, analysis, visualization management, analysis, visualization and use of chemical information.and use of chemical information.
In fact, Chemoinformatics is the application of informatics methods to solve chemical problems.
What is Chemoinformatics?What is Chemoinformatics?
Chemoinformatics, Cheminformatics, Chemical Informatics, Computational Chemistry, …
“the set of computer algorithms and tools to store and analyse chemical data in the context of drug discovery and design projects etc…”
4
What is Chemoinformatics?What is Chemoinformatics?
“the mixing of information resources to transform data into information and information into knowledge, for the intended purpose of making better decisions faster in the arena of drug lead identification and optimizaton”
5
What is Chemoinformatics?What is Chemoinformatics?
“chemoinformatics encompasses the design, creation, organisation, management, retrieval,analysis, dissemination, visualization and use
of chemical information”
6
Chemoinformatics : a new scienceChemoinformatics : a new science)?( )?(
7
Why do we need Why do we need ChemoinformaticsChemoinformatics??
To handle large amounts of information To move chemistry into the computer age
To move from data to knowledge.
9
And last but not least:
•To get funding (bioinformatics is doing well currently, whereas computational chemistry seems to be lagging behind).•Data information knowledge •measurements/calculations
Why do we need ChemoinformaticsWhy do we need Chemoinformatics?
10
How do we learn?How do we learn?
Inductive learning vs.. Inductive learning vs.. Deductive learningDeductive learning
Inductive learning vs. Deductive Inductive learning vs. Deductive learninglearning
Deductive learning:Deductive learning:A fundamental theory exists which allows us to calculate properties and predict the behavior of molecules. The fundamental theory for Chemistry is quantum mechanics.
Inductive learning vs. Deductive learningInductive learning vs. Deductive learningInductive learning = Learning from examplesInductive learning = Learning from examples
13
General scheme for inductive learningGeneral scheme for inductive learning
14
The fundamental tasks of a chemistThe fundamental tasks of a chemist property prediction, synthesis, design, reaction prediction, and
structure elucidation
15
The realm of ChemoinformaticsThe realm of Chemoinformatics
a) Representing Chemical Compounds
b) Searching Chemical Structuresc) Similarity Searchesd) Relating structure to properties with models
16
Machine Learning MethodsMachine Learning Methods
• Important role in chemoinformatics Important role in chemoinformatics – For example, it is usually difficult to
predict which types of descriptors are most suitable for a given search, classification.
• Therefore, machine learning techniques are often used to facilitate descriptor selection
17
Machine Learning Methods Machine Learning Methods – Genetic algorithms– Genetic algorithms
• Different parameters and model solutions to given problems are encoded in a chromosome and subjected to random variation, thus generating a population.
• Solutions provided by these chromosomes are evaluated by fitness function that assign high scores to desired results.
• Chromosomes yielding best intermediate solutions are subjected to mutation and crossover operation that correspond to random genetic mutations and gene recombination events.
• The resulting modified chromosomes represent the next generation and the process is continued until the obtained results meet a satisfactory convergence criterion
18
Quantitative Structure Activity Quantitative Structure Activity Relationship Analysis (QSAR)Relationship Analysis (QSAR)
Goal :Goal : Evaluation of molecular features that determine biological activity and the prediction of compound potency as a function of structural modification
19
Virtual Screening and Compound FilteringVirtual Screening and Compound Filtering
VS(Virtual Screening) - the process of screening large databases on the
computer for molecules having desired properties and biological activity.
A major application of VS techniques is the identification of novel active molecules in large compound databases.
20
Impact of new technology on drug discoveryImpact of new technology on drug discovery
• The last few years have seen a number of “revolutionary” new technologies:– Gene chips, genomics and HGP– Bioinformatics & Molecular biology– More protein structures– High-throughput screening & assays– Virtual screening and library design– Combinatorial chemistry– Other computational methods
• How do we make it all work for us?21
How Chemoinformatics can help outHow Chemoinformatics can help out
Producing and manage information for metrics to reduce risk, e.g.– Virtual screening– Library design,– Docking– Cost/benefit analysis
• Making information available at the right time and the right place Needs to be integrated into processes
22
Software relevance:Software relevance:Bridge between computation & scienceBridge between computation & science
clusteringsim. searchingactivity modelsscaffold detectiondockinglogp calculation
tasks:
“doing a cluster analysis”
“identifying activity-related fragments”
tools
chemoinformatics science
tasks:
work out a chemical synthesis
choose good reagents
try and document some reactions
goals:
e.g. produce compounds that have high biological activity
?
23
Chemoinformatics: WChemoinformatics: Where It Has here It Has Come From, Where It Is Now And Come From, Where It Is Now And
Where It Is GoingWhere It Is Going
OverviewOverviewFrom Chemical Information To From Chemical Information To
ChemoinformaticsChemoinformatics– Integration with techniques from molecular
modeling– Developments in computer hardware and software – Data explosion arising from developments in
combinatorial chemistry and high-throughput screening
25
Molecular ModellingMolecular Modelling
• Positioning of a putative ligand into a protein’s active site, first attempted by the DOCK program (UCSF, 1982)
• Initially restricted to rigid ligands and rigid proteins: current programs permit some degree of flexibility
• Use in structure-based design– Move from docking a single
ligand to sequential docking of large datasets
26
27
Graph TheoryGraph Theory• Graph theory is a branch of mathematics that
considers sets of objects, called nodesnodes, and the relationships, called edgesedges, between pairs of these objects
• The definition is completely general, allowing graphs to be used in many different application domains as long as an appropriate representation can be derived
28
Examples Of GraphsExamples Of Graphs
29
Proposed courses for a Distance Proposed courses for a Distance learning Programlearning Program
• Chemoinformatics Virtual ClassroomChemoinformatics Virtual Classroom
30
At present there are no specific software tools for chemical information training in the IranIran. A number of commercial software products used in the pharmaceutical and biotechnology industry are either too expensive or of limited utility for training in either academic or business settings. By employing distance learning distance learning through a web delivery system, the training software will provide an effective, low cost solution for academic institutions, whether they are offering a single course to students in a remote setting, or an entire program in cheminformatics.
31
32
In addition, such training tools will be very useful in industry settings with local area networks, where in a multidiscipline setting individuals need to receive training on the concepts employed by industrial chemoinformatics software's.
Chemoinformatics: aimsChemoinformatics: aims
• Develop an awareness of Informatics Management techniques used in the design and implementation of chemoinformatics systems
• Enable students to demonstrate skills learned by carrying out a small-scale industrially relevant chemoinformatics research project
• Basic structure– Three semesters of taught modules – One semester dissertation working at the site of
one of the companies supporting the programme33
Proposed Cources ;Proposed Cources ;
An introduction to chemoinformatics. – Chemoinformatics (Fundamental) – Information Systems Modelling – Information Storage and Retrieval– Foundations of Object-Oriented Programming
34
35
• Chemoinformatics (Advance ; more programming)
• Database Design • Research Methods and Dissertation
Preparation• Two from a range of elective modules,
including Molecular Modelling (Chemistry), Healthcare Information...etc
ConclusionsConclusions Distance learning is becoming increasingly accepted by the
professional bodies. The image of distance learning would need to be improved. The concept would have to be well presented as something new, modern and completely different from the old-style correspondence courses.
Chemoinformatics can step in to assist in this effort. And it can do so in all fields of chemistry, inorganic, analytical, organic, physical, medicinal, and bio-chemistry. And it can reach beyond chemistry provide methods and information that can be used in biology, medicine, and physics.
36
ReferencesReferencesJournal Articles
• Y. M. Alvarez-Ginarte,et al. Bioorganic & Medicinal Chemistry 16 (2008) 6448–6459.
• S. D. Lindell, L. C. Pattenden, J. Shannon, Bioorganic & Medicinal Chemistry 17 (2009) 4035–4046.
• J. Gasteiger, Chemometrics and Intelligent Laboratory Systems 82 (2006) 200 – 209.
37
ReferencesReferencesBooks• An introduction to chemoinformatics. A.R. Leach & V.J. Gillet.
Kluwer, 2003.• Chemoinformatics – A textbook. J. Gasteiger & T. Engel (eds).
Wiley-VCH, 2003.• Handbook of chemoinformatics. J. Gasteiger (ed.). Wiley-VCH,
2003.• Chemoinformatics: Concepts, Methods, and Applications (Methods
in MolecularBiology). J. Bajorath. Humana Press, 2004.• Molecular Modelling Principles and Applications. A. R. Leach.
Longman, 1996.
38
39
40
41
Chemoinformatics Chem(o)informatics is a generic
term that encompasses the; design, creation, organization, design, creation, organization,
management, analysis, visualization management, analysis, visualization and use of chemical information.and use of chemical information.
In fact, Chemoinformatics is the application of informatics methods to solve chemical problems.
What is Chemoinformatics?What is Chemoinformatics?
Chemoinformatics, Cheminformatics, Chemical Informatics, Computational Chemistry, …
“the set of computer algorithms and tools to store and analyse chemical data in the context of drug discovery and design projects etc…”
42
What is Chemoinformatics?What is Chemoinformatics?
“the mixing of information resources to transform data into information and information into knowledge, for the intended purpose of making better decisions faster in the arena of drug lead identification and optimizaton”
43
What is Chemoinformatics?What is Chemoinformatics?
“chemoinformatics encompasses the design, creation, organisation, management, retrieval,analysis, dissemination, visualization and use
of chemical information”
44
Chemoinformatics : a new scienceChemoinformatics : a new science)?( )?(
45
Why do we need Why do we need ChemoinformaticsChemoinformatics??
To handle large amounts of information To move chemistry into the computer age
To move from data to knowledge.
47
And last but not least:
•To get funding (bioinformatics is doing well currently, whereas computational chemistry seems to be lagging behind).•Data information knowledge •measurements/calculations
Why do we need ChemoinformaticsWhy do we need Chemoinformatics?
48
How do we learn?How do we learn?
Inductive learning vs.. Inductive learning vs.. Deductive learningDeductive learning
Inductive learning vs. Deductive Inductive learning vs. Deductive learninglearning
Deductive learning:Deductive learning:A fundamental theory exists which allows us to calculate properties and predict the behavior of molecules. The fundamental theory for Chemistry is quantum mechanics.
Inductive learning vs. Deductive learningInductive learning vs. Deductive learningInductive learning = Learning from examplesInductive learning = Learning from examples
51
General scheme for inductive learningGeneral scheme for inductive learning
52
The fundamental tasks of a chemistThe fundamental tasks of a chemist property prediction, synthesis, design, reaction prediction, and
structure elucidation
53
The realm of ChemoinformaticsThe realm of Chemoinformatics
a) Representing Chemical Compounds
b) Searching Chemical Structuresc) Similarity Searchesd) Relating structure to properties with models
54
Machine Learning MethodsMachine Learning Methods
• Important role in chemoinformatics Important role in chemoinformatics – For example, it is usually difficult to
predict which types of descriptors are most suitable for a given search, classification.
• Therefore, machine learning techniques are often used to facilitate descriptor selection
55
Machine Learning Methods Machine Learning Methods – Genetic algorithms– Genetic algorithms
• Different parameters and model solutions to given problems are encoded in a chromosome and subjected to random variation, thus generating a population.
• Solutions provided by these chromosomes are evaluated by fitness function that assign high scores to desired results.
• Chromosomes yielding best intermediate solutions are subjected to mutation and crossover operation that correspond to random genetic mutations and gene recombination events.
• The resulting modified chromosomes represent the next generation and the process is continued until the obtained results meet a satisfactory convergence criterion
56
Quantitative Structure Activity Quantitative Structure Activity Relationship Analysis (QSAR)Relationship Analysis (QSAR)
Goal :Goal : Evaluation of molecular features that determine biological activity and the prediction of compound potency as a function of structural modification
57
Virtual Screening and Compound FilteringVirtual Screening and Compound Filtering
VS(Virtual Screening) - the process of screening large databases on the
computer for molecules having desired properties and biological activity.
A major application of VS techniques is the identification of novel active molecules in large compound databases.
58
Impact of new technology on drug discoveryImpact of new technology on drug discovery
• The last few years have seen a number of “revolutionary” new technologies:– Gene chips, genomics and HGP– Bioinformatics & Molecular biology– More protein structures– High-throughput screening & assays– Virtual screening and library design– Combinatorial chemistry– Other computational methods
• How do we make it all work for us?59
How Chemoinformatics can help outHow Chemoinformatics can help out
Producing and manage information for metrics to reduce risk, e.g.– Virtual screening– Library design,– Docking– Cost/benefit analysis
• Making information available at the right time and the right place Needs to be integrated into processes
60
Software relevance:Software relevance:Bridge between computation & scienceBridge between computation & science
clusteringsim. searchingactivity modelsscaffold detectiondockinglogp calculation
tasks:
“doing a cluster analysis”
“identifying activity-related fragments”
tools
chemoinformatics science
tasks:
work out a chemical synthesis
choose good reagents
try and document some reactions
goals:
e.g. produce compounds that have high biological activity
?
61
Chemoinformatics: WChemoinformatics: Where It Has here It Has Come From, Where It Is Now And Come From, Where It Is Now And
Where It Is GoingWhere It Is Going
OverviewOverviewFrom Chemical Information To From Chemical Information To
ChemoinformaticsChemoinformatics– Integration with techniques from molecular
modeling– Developments in computer hardware and software – Data explosion arising from developments in
combinatorial chemistry and high-throughput screening
63
Molecular ModellingMolecular Modelling
• Positioning of a putative ligand into a protein’s active site, first attempted by the DOCK program (UCSF, 1982)
• Initially restricted to rigid ligands and rigid proteins: current programs permit some degree of flexibility
• Use in structure-based design– Move from docking a single
ligand to sequential docking of large datasets
64
65
Graph TheoryGraph Theory• Graph theory is a branch of mathematics that
considers sets of objects, called nodesnodes, and the relationships, called edgesedges, between pairs of these objects
• The definition is completely general, allowing graphs to be used in many different application domains as long as an appropriate representation can be derived
66
Examples Of GraphsExamples Of Graphs
67
Proposed courses for a Distance Proposed courses for a Distance learning Programlearning Program
• Chemoinformatics Virtual ClassroomChemoinformatics Virtual Classroom
68
At present there are no specific software tools for chemical information training in the IranIran. A number of commercial software products used in the pharmaceutical and biotechnology industry are either too expensive or of limited utility for training in either academic or business settings. By employing distance learning distance learning through a web delivery system, the training software will provide an effective, low cost solution for academic institutions, whether they are offering a single course to students in a remote setting, or an entire program in cheminformatics.
69
70
In addition, such training tools will be very useful in industry settings with local area networks, where in a multidiscipline setting individuals need to receive training on the concepts employed by industrial chemoinformatics software's.
Chemoinformatics: aimsChemoinformatics: aims
• Develop an awareness of Informatics Management techniques used in the design and implementation of chemoinformatics systems
• Enable students to demonstrate skills learned by carrying out a small-scale industrially relevant chemoinformatics research project
• Basic structure– Three semesters of taught modules – One semester dissertation working at the site of
one of the companies supporting the programme71
Proposed Cources ;Proposed Cources ;
An introduction to chemoinformatics. – Chemoinformatics (Fundamental) – Information Systems Modelling – Information Storage and Retrieval– Foundations of Object-Oriented Programming
72
73
• Chemoinformatics (Advance ; more programming)
• Database Design • Research Methods and Dissertation
Preparation• Two from a range of elective modules,
including Molecular Modelling (Chemistry), Healthcare Information...etc
ConclusionsConclusions Distance learning is becoming increasingly accepted by the
professional bodies. The image of distance learning would need to be improved. The concept would have to be well presented as something new, modern and completely different from the old-style correspondence courses.
Chemoinformatics can step in to assist in this effort. And it can do so in all fields of chemistry, inorganic, analytical, organic, physical, medicinal, and bio-chemistry. And it can reach beyond chemistry provide methods and information that can be used in biology, medicine, and physics.
74
ReferencesReferencesJournal Articles
• Y. M. Alvarez-Ginarte,et al. Bioorganic & Medicinal Chemistry 16 (2008) 6448–6459.
• S. D. Lindell, L. C. Pattenden, J. Shannon, Bioorganic & Medicinal Chemistry 17 (2009) 4035–4046.
• J. Gasteiger, Chemometrics and Intelligent Laboratory Systems 82 (2006) 200 – 209.
75
ReferencesReferencesBooks• An introduction to chemoinformatics. A.R. Leach & V.J. Gillet.
Kluwer, 2003.• Chemoinformatics – A textbook. J. Gasteiger & T. Engel (eds).
Wiley-VCH, 2003.• Handbook of chemoinformatics. J. Gasteiger (ed.). Wiley-VCH,
2003.• Chemoinformatics: Concepts, Methods, and Applications (Methods
in MolecularBiology). J. Bajorath. Humana Press, 2004.• Molecular Modelling Principles and Applications. A. R. Leach.
Longman, 1996.
76
77
78
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