1 PowerMV Chemical Data Mining Environment S. Stanley Young Jun Feng and Jack Liu NISS MPDM, McMaster University 4 June 2005.

Slides:

Advertisements

Similar presentations

JKlustor clustering chemical libraries presented by … maintained by Miklós Vargyas Last update: 25 March 2010.

Advertisements

SOMA2 – Drug Design Environment. Drug design environment – SOMA2 The SOMA2 project Tekes (National Technology Agency of Finland) DRUG2000 program.

UGM, June, 2007 Presenting: Szabolcs Csepregi JChem Base and Cartridge latest.

1 Schedule 8:30-9:30 Introduction 9:40- 10:45 Analysis Methods 10:55-12:00 Design and Analysis 12:00 Lunch 1:00-2:05 Design and Analysis I (Will and Stan)

1 Sequential Screening S. Stanley Young NISS HTS Workshop October 25, 2002.

C2D Cheminformatics : Methods,Tools and Results By OSDD-Cheminformatics team.

PharmaMiner: Geometric Mining of Pharmacophores 1.

Linking Genetic Profiles to Biological Outcome Paul Fogel Consultant, Paris S. Stanley Young National Institute of Statistical Sciences NISS, NMF Workshop.

1 PharmID: A New Algorithm for Pharmacophore Identification Stan Young Jun Feng and Ashish Sanil NISSMPDM 3 June 2005.

Jeffery Loo NLM Associate Fellow ’03 – ’05 chemicalinformaticsforlibraries.

1CBS, Department of Systems Biology Exercise : Drug-likeness by ’rule of five’ Log into your databar account, start Firefox and go to the following web-

Spatial Outlier Detection and implementation in Weka Implemented by: Shan Huang Jisu Oh CSCI8715 Class Project, April Presented by Jisu.

Exploring Chemical Space with Computers—Challenges and Opportunities Pierre Baldi UCI.

1 BrainWave Biosolutions Limited Accelerating Life Science Research through Technology.

3. Chemical Data and Data Bases. 2 Datasets and Databases Many small datasets are available Several commercial databases of compounds and reactions (e.g.

341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London

Cédric Notredame (30/08/2015) Chemoinformatics And Bioinformatics Cédric Notredame Molecular Biology Bioinformatics Chemoinformatics Chemistry.

Module 2: Structure Based Ph4 Design

Molecular Descriptors

Combinatorial Chemistry and Library Design

Topological Summaries: Using Graphs for Chemical Searching and Mining Graphs are a flexible & unifying model Scalable similarity searches through novel.

Chapter 13 Genetic Algorithms. 2 Data Mining Techniques So Far… Chapter 5 – Statistics Chapter 6 – Decision Trees Chapter 7 – Neural Networks Chapter.

Similarity Methods C371 Fall 2004.

1 Mean shift and feature selection ECE 738 course project Zhaozheng Yin Spring 2005 Note: Figures and ideas are copyrighted by original authors.

A hybrid method for Mining Concepts from text CSCE 566 semester project.

Introduction to Chemoinformatics Irene Kouskoumvekaki Associate Professor December 12th, 2012 Biological Sequence Analysis course.

Fusing database rankings in similarity-based virtual screening Peter Willett, University of Sheffield.

Copyright Elsevier MDL 2007 Present and future of informatics in chemistry Symposium in Honor of Gary Wiggins Division of Chemical Information 223 rd ACS.

Intralab Workshop - Reactome CMAP Chang-Feng Quo June 29 th, 2006.

Indices Tomasz Bartoszewski. Inverted Index Search Construction Compression.

Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis) 

ChemModLab: A Web-based Cheminformatics Modeling Laboratory S. Stanley Young + ECCR and ChemSpider Teams.

Use of Machine Learning in Chemoinformatics Irene Kouskoumvekaki Associate Professor December 12th, 2012 Biological Sequence Analysis course.

Analysis of Complex Proteomic Datasets Using Scaffold Free Scaffold Viewer can be downloaded at:

Open source software and web services for designing therapeutic molecules G. P. S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology,

Emergence of Scaling and Assortative Mixing by Altruism Li Ping The Hong Kong PolyU

In silico discovery of inhibitors using structure-based approaches Jasmita Gill Structural and Computational Biology Group, ICGEB, New Delhi Nov 2005.

ChemBank Building a Public Web Resource Using Daycart Erik Brauner Head of Chemical and Biological Computing Harvard Institute of Chemistry and Cell Biology.

QSAR Study of HIV Protease Inhibitors Using Neural Network and Genetic Algorithm Akmal Aulia, 1 Sunil Kumar, 2 Rajni Garg, * 3 A. Srinivas Reddy, 4 1 Computational.

SRI International Bioinformatics 1 SmartTables & Enrichment Analysis Peter Karp SRI Bioinformatics Research Group September 2015.

Graduate Seminar Ka-Lok Ng Dept. of Bioinformatics, Asia University x1856 Room i 408

University at BuffaloThe State University of New York Lei Shi Department of Computer Science and Engineering State University of New York at Buffalo Frequent.

Vocabulary in VB So Far. Assignment: Used to change the value of an object at run time Used to change the value of an object at run time.

NA-MIC National Alliance for Medical Image Computing Using Annotations in Slicer 4.0 Yong Zhang, Kilian Pohl June 2010.

Structural Models Lecture 11. Structural Models: Introduction Structural models display relationships among entities and have a variety of uses, such.

Selecting Diverse Sets of Compounds C371 Fall 2004.

PharmaMiner: Geometric Mining of Pharmacophores 1.

1 High Throughput Target Identification Stan Young, NISS Doug Hawkins, U Minnesota Christophe Lambert, Golden Helix Machine Learning, Statistics, and Discovery.

Introduction to Chemoinformatics and Drug Discovery Irene Kouskoumvekaki Associate Professor February 15 th, 2013.

Annotation by category – ELAN and ISO DCR Han Slöetjes, Peter Wittenburg Max-Planck-Institute for Psycholinguistics LREC,

Use of Machine Learning in Chemoinformatics

G LOBAL S IMILARITY B ETWEEN M ULTIPLE B IONETWORKS Yunkai Liu Computer Science Department University of South Dakota.

Identification of structurally diverse Growth Hormone Secretagogue (GHS) agonists by virtual screening and structure-activity relationship analysis of.

Computational Approach for Combinatorial Library Design Journal club-1 Sushil Kumar Singh IBAB, Bangalore.

Molecular mechanics Classical physics, treats atoms as spheres Calculations are rapid, even for large molecules Useful for studying conformations Cannot.

1 Survey of Biodata Analysis from a Data Mining Perspective Peter Bajcsy Jiawei Han Lei Liu Jiong Yang.

A Computational Study of RNA Structure and Dynamics Rhiannon Jacobs and Harish Vashisth Department of Chemical Engineering, University of New Hampshire,

Introduction to PubChem BioAssay

Outline Introduction NMF Chemistry Problem

Hanan Ayad Supervisor Prof. Mohamed Kamel

The method to Take down the printer's model number and on your computer Download Drivers For a Lexmark Laser Printer.

Topological Ordering Algorithm: Example

Visualization of Content Information in Networks using GlyphNet

Topological Ordering Algorithm: Example

Topological Ordering Algorithm: Example

Applying principles of computer science in a biological context

Tantan Liu, Fan Wang, Gagan Agrawal The Ohio State University

Topological Ordering Algorithm: Example

Derivatives and Gradients

Presentation transcript:

1 PowerMV Chemical Data Mining Environment S. Stanley Young Jun Feng and Jack Liu NISS MPDM, McMaster University 4 June 2005

2 Outline 1.PowerMV, a chemistry data mining environment. 2.rSVD, robust singular value decomposition, Liu, Hawkins, Ghosh,Young, PNAS (2003). 3.Space-filling designs. 4.PharmID: complex problem.

3 Environment 20k lines of interface code; 300k lines of algorithm code. ~0.75 man-years.

4 SD File, 50 years old and bad! 1 -ISIS- 3D V C N C C C C N C C S C C C C C C C C C C Etc.

5 Smiles Chemical Notation CC1=CC=C(C=C1)S(=O)(=O)N(CC(O)=O)C2=CC(Cl)=CC=C2 CC1CCC(CC1)C(C)(C)C(CC(C)C)C2CCCC(C)C2

6 Viewer

7 Molecule Blow Up

8 3D View

9 Compute Molecular Descriptors, Drug-Like Properties

10 Chemical Graphs and Properties

11 Multiple Descriptor Types Numerical Topology!

12 Similarity Searching, Motivating Paper

13 Select a Target Compound

14 Search Dialog

15 Structure Comparison Window Target Neighbor Annotation

16 Statistical Methods

17 Free download : Summary Display SD. Compute descriptors. Cluster. Statistical analysis. Similarity search. Become NISS affiliate! 20k display code 300k algorithm code

18 Contact Information Stan Young Jun Feng Become a NISS Affiliate!

19 Questions / Comments ?

20 Computed Properties – Rule of 5

21 Structure Comparison

22 Neighbor List

23 Attribute Comparison

24 Annotated Data Bases 1.Stockwell ACL 2.ChemBank 3.Exploratory Centers for Chemoinformatics Research 4.Chemical Entities of Biological Interest 5.Commercial, e.g. GVK, ACS, MDDR, Ashgate

25 Rule of Five

26 Example: CNS Compounds

27 Current NISS Research PharmID: Pharmacophore Identification Finds multiple binding modes! Selectivity. 1.NISS research. 2.Jun Feng, CompChem. 3.Seeking collaborators. 4.Become NISS affiliate.