- Email: [email protected]
October 2000 International Workshop on Methods for Macromolecular Modelling (M3)
Induced Fit in Database Screening
and Chemistry, 2 University of Minnesota, St. Paul~Minneapolis, MN55455 USA. [email protected], [email protected]
Analysis of amide hydrogen exchange rates in proteins leads us to expect that the slow exchange core is the folding core; that is, elements of secondary structure that compose the slow exchange core are expected to favor native-like structure early in folding, and when synthesized as core peptides. Experimental approaches to test implications of these generalizations employ derivatives of the protein BPTI (bovine pancreatic trypsin inhibitor). (i) The ensemble structure,'folding and dynamics of partially folded and completely unfolded BPTI species synthesized by solid phase methods are characterized by NMR. Partially folded BPTI having one disulfide outside the core, and missing two disulfides within the core, is most organized in the core. In the partially folded ensemble, each NH undergoes slow, local conformational exchange between two structural families, Pf (more ordered) and Pd (random coil-like). This may be general for partially folded proteins. (ii) Core modules, peptides modelling the protein core, sample a broad array of conformations, but tend to favor native-like organization. (iii) Core modules have been covalently linked in an attempt to produce an N state, in which one conformation is substantially more stable than all other accessible conformations. (iv) Dynamics and structure of a BPTI mutant perturbed outside the core have been determined. Mutant G37A is destabilized by about 5 kcal/mol relative to WT, and is unusual in BPTI mutants in exhibiting rollover kinetics in denaturant-dependent chevron plots. Although G37A has the same average NMR structure as WT, it also has substantial increases in internal motion, indicated by hydrogen exchange rates and aromatic ring flips.
Structure and Dynamics of 6-Hydroxymethyl7, 8-dihydropterin Pyrophosphokinase
Maria L Zavodszky, Paul C. Sanschagrin, and Leslie A. Kuhn, Department of Biochemistry, Michigan State University, East Lansing, M148824. http://www.bch.msu.edu/labs/kuhn
It is widely accepted that flexibility is indispensable for protein function. One primary function of a protein is to recognize and bind other molecules. The question is how much flexibility is needed, in general, for protein-ligand interactions, and how this flexibility partitions between the protein and its ligand. Most algorithms designed to identify and dock ligands handle the proteins themselves as rigid bodies. Those that do take into account induced complementarity upon interaction use either side chain rotamer libraries or other sampling techniques and are too slow for use in molecular screening. Our screening program, SLIDE (Screening for Ligands by Induced-fit Docking Efficiently), models flexibility by allowing both protein side chain rotations and full ligand flexibility. Our starting assumption is that both the protein and the ligand change their conformation as little as possible upon binding to each other. SLIDE reduces the large number of ligand candidates to a manageable number using distance geometry techniques to compare inter-atomic distances and number of hydrogen bond donors and acceptors of each ligand with those in the template representing the binding site. Mean-field theory is used to select minimal directed rotations of bonds both in the ligand and the protein side chains to resolve interatomic collisions between the target and those ligands that have a complementary shape and chemistry. Each collisionfree ligand orientation is scored based on the number of hydrogen bonds and the hydrophobic complementarity with the protein. Results on screening for ligands to thrombin indicate that our assumption of minimal motion works well in this case.
Honggao YanI, Genbin Shi. i Jaroslaw Blaszczyk, 2 Bin Xiao, 2 and Xinhua Ji, 21Department of Biochemistry, Michigan State University, East Lansing, M148824 USA, 2Program in Structural Biology, National Cancer Institute, P.O. Box B, Frederick, MD 21702 USA
UPCOMING MEETINGS
6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate biosynthetic pathway. Folate cofactors are essential for life. Mammals derive folates from their diets, whereas most microorganisms must synthesize folates de novo. HPPK is therefore an ideal target for the development of novel antimicrobial agents. As a small (158 residues, ~ 18 kDa), stable, monomeric protein, E. coli HPPK is also an excellent model system for studying the mechanisms of enzymatic pyrophosphoryl transfer. The structures of apoHPPK and many complexes have been determined by x-ray crystallography and multidimensional multinuclear NMR spectroscopy. The structural studies have revealed not only the detailed interactions between the substrates and the enzymes but also dramatic,unusual conformational and dynamical changes upon binding the substrates or substrate analogs.
International Workshop on Methods for Macromolecular Modelling (M 3)
558
October 2 0 0 0
Courant Institute o f Mathematical Sciences N e w York, NY, USA October 12-14, 2000
The purpose of the multidisciplinary workshop is to bring together both developers of computational tools for biomolecular simulations and those biological and chemical scientists who use computer modelling to macromolecular problems. The workshop will be co-sponsored by Society for Industrial and Applied Mathematics.
.J. Mol. Graphics Mod., 2000, Vol. 18, August-October
Topics Long-term molecular dynamics simulations • Conformational sampling: equilibrium and nonequilibrium processes •
• Multiscale modelling • Quantum/classical mechanics • Fast electrostatics applications to DNA modelling, enzyme catalysis, and DNA/protein systems The program will provide an opportunity for scientific exchange among biomolecular researchers, computer scientists, and applied mathematicians. Applied mathematicians and computer scientists will benefit from direct interaction with the modelers, and biochemical modelers will be exposed to recent developments in numerics and algorithms from which their studies can benefit. The will stimulate and integrate ideas from disparate disciplines, educate young investigators interested in the field, and assess current progress as well as pinpoint future directions for the field through a Perspectives session at the end of the workshop. Articles by invited speakers will be collected in Springer Verlag's Lecture Notes series in Computational Science & Engineering (LNCSE), edited by members of the organizing committee.
Contact Dr. Tamar Schlick Courant Institute of Mathematical Sciences New York University 251 Mercer Street New York, NY 10012 Tel: 212-998-3116 Fax: 212-995-4152
workshop @biomath, nyu. edu http://monod, biomath, nyu. edu/-hgan/conf_O0, html
• Ken Dill, University Of California, San Francisco • Robert Fletterick, University Of California, San Francisco • Simon Kearsley, Merck • Peter Kollman, University Of California, San Francisco • Irwin Kuntz, University Of California, San Francisco • Jon Mason, Bristol-Myers Squibb • Ken Merz, Pharmacopeia • David Pearlman, Vertex Pharmaceuticals • Tom Scanlan, University Of California, San Francisco • Bruce Tidor, Massachus.etts Institute of Technology • Dennis Underwood, DuPont Pharmaceuticals • Gennady Verkhivker, Agouron • Jim Wells, Sunesis Pharmaceuticals
Contact Kristina Clarke University of California, San Francisco Department of Pharmaceutical Chemistry 513 Parnassus Avenue, Room S-926, San Francisco, CA 94143-0446 USA Tel: 415-514-0148 Fax: 415-502-4690 kristina @cgl. ucsf edu http://mdi.ucsf edu/
Computational Genomics October 26-31, 2000 Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724 USA
Drug Design and Discovery
Instructors
October 13-14, 2000 University of California, San Francisco Laurel Heights Conference Center 3333 California St. San Francisco, CA 94118 USA
• William Pearson, University of Virginia, Charlottesville • Randall Smith, SmithKiine Beecham Pharmaceuticals This course presents a comprehensive overview of the theory and practice of computational methods for gene identification and characterization from DNA sequence data. It focuses on approaches for extracting the maximum amount of information from protein and DNA sequence similarity through sequence database searches, statistical analysis, and multiple sequence alignment. Additional topics are gene recognition, exon/intron prediction, identifying signals in unaligned sequences, and integration of genetic and sequence information in biological databases. Lectures are combined with hands-on exercises; students are encouraged to use their own data. The course is designed for biologists seeking advanced training in biological sequence analysis, computational biology core resource directors and staff, and for scientists in other disciplines, such as computer science, who wish to survey current research problems in biological sequence analysis.
Topics • Drug Design and Discovery • Medicinal and Pharmaceutical Chemistry The meeting will provide many interesting perspectives on how the science and the technology of drug discovery are changing and will continue to change in the era of combinatorial chemistry and genomics. The meeting is sponsored by the Department of Pharmaceutical Chemistry and the Molecular Design Institute of the University of California, San Francisco. The meeting is chaired by Professors Peter Kollman, Ken Dill, and Irwin (Tack) Kuntz who have brought together an impressive group of speakers to describe challenges in using current technologies and needs and prospects for the future.
Speakers • Paul Anderson, Senior VP Chemical and Physical Sciences, DuPont Pharmaceuticals
• Johan Aqvist, Uppsala University • Fred Cohen, University Of California, San Francisco
Contact Course Registrar Cold Spring Harbor Laboratory Meetings & Courses Office 1 Bungtown Road Cold Spring Harbor, NY 11724 USA
J. Mol. Graphics Mod., 2000, Vol. 18, August-October
559
meetings @cshl. org http://nucleus, cshl. org/meetings/2OOOc-info, htm
November 2000
Ninth Conference on Current Trends in Computational Chemistry November 3-4, 2000 Vicksburg, Mississippi, USA This .symposium will cover all areas of computational chemistry as well as quantum chemistry.
Invited Speakers • • • • • • • • • • •
Benoit Champagne, University Notre-Dame de la Paix Jurgen Gauss, Mainz University Ilya Kaplan, University of Mexico Jerome Karle, Naval Research Laboratory Iwao Ohmine, Nagoya University Mark Olson, Biomedical Supercomputer Center Roman Osman, Mt. Sinai School of Medicine Michele Parrinello, Max-Planck Institute Andrzej Sadlej, Nicolaus Copernicus University at Torun Henry F. Schaefer III, University of Georgia Vladimir Spirko, Hejrovsky Institute of Physical Chemistry • Robert E. Wyatt, University of Texas at Austin • Tom Ziegler, University of Calgary
Contact Department of Chemistry, Jackson State University, Jackson, MS 39217 USA Conference Chairman: Jerzy Leszczynski, Tel: 601-979-3482
jerzy2, iris5.jsums, edu Conference Secretary: Ms. Shonda R. Allen, Tel: 601-979-3723 srallen @stallion.jsums, edu http://ccmsi, jsums.edu/cctcc/
• Juan Enriquez, Senior Researcher, Genomics, Harvard Business School, USA • John G. Sgouros, Head of Computational Genome Analysis Laboratory, Imperial Cancer Research Fund, London, UK • Klaus Lindpaintner, Director and Vice President, Roche Genetics (Europe), F. Hoffman La Roche, Switzerland
Contact www. ibc-biomics, corn
December 2000
6th Australian Molecular Modelling Workshop (MM2000) December 5-8, 2000 RMIT University Melbourne, Australia
Topics • • • •
Colloid and Surface Chemistry Drug Design and Discovery Medicinal and Pharmaceutical Chemistry Surfactants, Molecular Modelling, Genomics
Session Titles • • • • • • • • • •
First Principles Molecular Dynamics Non-equilibrium Molecular Dynamics Quantum Chemistry Atomistic Simulations of Solids Surfaces and Interfaces Polymer Modelling Drug Design Protein Modelling Genomic Analysis Bioinformatics
Contact
November 13-16, 2000 Messe Stuttgart International Stuttgart, Germany
Molecular Modelling Workshop Anjani Singh Department of Applied Physics RMIT, GPO Box 2476V Melbourne, Victoria 3001, Australia Tel: 61 3 9925 2600 Fax: 61 3 9925 5290
Topics
mm2000 @rmit. edu. au http://www.ph, rmit. edu. au/mm2000
Biomics
• Genomic and proteomic technology • Agrogenomics • New and exciting topics on structural biology and in silico biology • Bioinformatics • Applications • Licensing workshop
Speakers • Leroy Hood, President and Director, Institute for Systems Biology, USA • Denis Hochstrasser, Geneva Proteomics, Geneva, Switzerland
560
J. Mol. Graphics Mod., 2000, Vol. 18, August-October
Critical Assessment of Techniques for Free Energy Evaluation December 7-8, 2000 Asilomar Conference Center Asilomal; CA USA
Topics Biological Chemistry, techniques for predicting energies of binding and solvation CATFEE is a challenge and meeting designed to assess and discuss the techniques employed in computer assisted drug
design efforts. CATFEE will provide the opportunity to modelers and experimentalists to test new algorithms and evaluate established techniques used for the prediction of binding free energies.
January 2001
Contact
January 24-26, 2001 SwissOtel Zurich Am Marktplatz Oerlikon CH-8050 Zurich, Switzerland
CATFEE Tel: 323-995-6599 catfee @uqbat: ncifclf go v http://uqbar.ncifcrf gov/~catfee/
Gene Function Prediction GeneRAGE: Algorithm for Sequence Clustering and Domain Detection Dr Cristos Ouzounis, EB[
Structure-based Drug Design December 13-15, 2000 St. Catherine's College Oxford, UK
Automatic Discovery of Regulatory Patterns in Promoter Regions Based on Whole Cell Expression Data and Functional Annotation Dr. Steen Knudsen, Technical University of Denmark
Topics Computational Chemistry, Drug Design and Discovery
Target Gene Identification from Expression Array Data by Promoter Analysis Dr. TITomas Werner, Genomatix Software GmbH
Session Titles • • • • •
Integrative Bioinformatics High.Throughput Interpretation of Pathways and Biology
Principles and applications of structure based drug design Advances in computational methods Advances in experimental methods New drug targets Combinatorial Chemistry, Genomics and Proteomics
Combining Gene-Finding Programs to Increase Prediction Accuracy Dr. Cecilia Hammar, University of SkOvde (tentative) Functional Gene Networks: A Case Study of a Novel Data Management Approach for Bioinformatics Dr. Stephan Heymann, Kehnan Gesellschaft fiir Geninformation mbH
Contact Rebecca Wade The Molecular Graphics and Modelling Society, UK wade @embl-heidelbe rg. de h ttp://ww w.mgms. org/oxford2000/
Stability and Flexibility of Cellular Pathways Dr. Rajah Kumar, Sarnoff Corporation
Structural Genomics A Comprehensive Database of Protein Structure Models for Drug Discovery Dr. Tod M. Klingler, Prospect Genomics, Inc.
GRID 2000: International Workshop on Grid Computing in Conjunction with the 7th International Conference on High Performance Computing
The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli Dr. Sarah A. Teichmann, University College London
December 17-20, 2000 Bangalore, India
Topics Computational Chemistry, Grid Fabrics and Architectures
Sponsors • IEEE Computer Society • ACM SIGARCH GRID 2000 is an international meeting that brings together international grid computing researchers, developers, practitioners, and users. The aim of GRID 2000 is to serve as a forum to present current and future work as well as to exchange research ideas in this field.
Structural Pattern Localization Analysis by Sequential Histograms Speaker to Be Determined, IBM, T.J. Watson Research Center (tentative)
Visualizing Gene Expression Data Microarray Analysis as Module of LION's Integrated Life Science Informatic Platform Dr. Jan Michel, LION Bioscience AG A Decision Analytics Framework for Bioinformatics Dr Mark Demesmaeker, Spo~ire Inc. High-Throughput Research Using Microarray Gene Expression Information Dr. Frank A. White, InforMax, Inc.
Contact Rajkumar Buyya GRID Monash University Clayton Campus School of Computing Science and Software Engineering Melbourne, Australia
Gene Profiling for Target Identification New Bioinformatics Approaches in Functional Genomics Dr. Jean-Michel Claverie, CNRS
http://www, buyya, o rg/Grid2000/
Human Adult Skeletal Muscle Transcriptional Profile
J. Moi. Graphics Mod., 2000, Vol. 18, August-October
561
Reconstructed by Novel Computational Approach Prof. Gian Antonio Danieli, University of Padua
• Darren Green, GlaxoWellcome • lain Mclay, GlaxoWellcome • Dave Brown, Pfizer
Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation
Contact
Dr. Charles A. Mein, University of Cambridge (invited)
Dr. Darren Flower Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK Tel: +44 1635 577954 Fax: +44 1635 577954
Protein Expression
Proteins Have a Diverse and Distinct Repertoire of Interactions
Dr. Michael Lappe, European Bioinformatics Institute
darren.flower@jennerac, uk
Analysis of the Transcriptome by a Combined Approach
Dr. Alon Amit, Compugen
April 2001
Mining Mass Spectrometric Data for Disease Biomarkers
221th American Chemical Society (ACS) National Meeting
Dr. Pierre Huyn, SurroMed, Inc. Computational
Genomics
April 1-6, 2001 San Diego, CA USA
Genome-to-Genome Comparisons Using Terablast
Mr. Marry Gollery, TimeLogic, hw. Fast Probabilistic Analysis of Sequence Function Using Scoring Matrices
Contact American Chemical Society Meetings Department 1155 Sixteenth Street, N.W. Washington, DC 20036 USA Tel: 202-872-4396 Fax: 202-872-6128
Dr. Craig NeviU-Manning, Rutgers University (tentative) System for Integrating Data on GABA Receptors Dr. Hannah Hong Xue, The Hong Kong University of Science and Technology
[email protected]
Genomic Discoveries Quickly Converted into SmallMolecule Drug-Discovery Programs
Second Joint Sheffield Conference on Chemoinformatics: Computational Tools for Lead Discovery
Speaker to Be Determined, Iconix Pharmaceuticals, Inc.
Contact Christina Lingham 1037 Chestnut St. Newton Upper Falls, MA 02464 USA Tel: 617-630-1364 Fax: 617-630-1325
cling ham @healthtech, cam www.healthtech, com/2OO1/bne/index, htm
March 2001
Cutting Edge Approaches to Drug Design March 13, 2001 Scientific Societies Lecture Theatre Seville Row, London, UK This meeting addresses methods of drug design at the cutting edge: molecular simulation, knowledge management, and informatics. A key objective of the meeting is to explore how synergistic collaboration between informaticians and the experimental chemist can transform the speed and profitability of the pre-clinical pharmaceutical research process. The meeting is organized by the Royal Society of Chemistry through the Biological and Medicinal Chemistry Sector and Molecular Modelling Group.
April 9-11, 2001 Stephenson Hall University of Sheffield, UK The conference will cover all aspects of lead discovery including: • 3D databases, including docking and pharmacophore analysis • Assay QC and its influence on data mining • Chemical data mining • Descriptor validation • Design of leadlike combinatorial libraries • Design of screening collections • e-business to facilitate lead discovery • Novel software and hardware systems for lead discovery • Selective compound acquisition from in house and commercial suppliers • Similarity and clustering methods • Structure-activity methods for lead identification and early optimization • Structure-based design for lead identification and early optimization • Virtual screening • Case histories
Provisional Speakers List
Contact
• Prof. Sir Tom Blundell, FRS • Andy Lyall, Oxford GlycoSciences • Andy Davis, AstraZeneca
Val Gillet
562
.J. Mol. Graphics Mod., 2000, Vol. 18, August-October
v.gillet @sheffield.ac, uk www.shef. ac. uk/cisrg/shef2001
Magnetic Resonance in Chemistry and Biology April 20-27, 2001 Zvenigorod Russian Federation The aim of the Xlth conference is to bring together scientists interested in the development of Magnetic Resonance techniques and experimental methods and their applications in chemical and biological research.
Session Titles • Nitric oxide in chemistry and biology • Advanced NMR imaging in biomedical fields • The environment and magnetic resonance research Contact Dr. Vladimir Sharygin
Institute of Chemical Physics of Russian Academy of Sciences Kosygin's Street 4 Moscow Russian Federation 117977
http ://www. chem.msu, su/eng/events/zveni gOl.html
July 2001 Intelligent Systems for Molecular Biology July 21-25, 2001 Copenhagen, Denmark Contact Johanne Keiding
johanne @cbs. dtu. dk
J. Mol. Graphics Mod., 2000, Vol. 18, August-October
563
and Chemistry, 2 University of Minnesota, St. Paul~Minneapolis, MN55455 USA. [email protected], [email protected]
Analysis of amide hydrogen exchange rates in proteins leads us to expect that the slow exchange core is the folding core; that is, elements of secondary structure that compose the slow exchange core are expected to favor native-like structure early in folding, and when synthesized as core peptides. Experimental approaches to test implications of these generalizations employ derivatives of the protein BPTI (bovine pancreatic trypsin inhibitor). (i) The ensemble structure,'folding and dynamics of partially folded and completely unfolded BPTI species synthesized by solid phase methods are characterized by NMR. Partially folded BPTI having one disulfide outside the core, and missing two disulfides within the core, is most organized in the core. In the partially folded ensemble, each NH undergoes slow, local conformational exchange between two structural families, Pf (more ordered) and Pd (random coil-like). This may be general for partially folded proteins. (ii) Core modules, peptides modelling the protein core, sample a broad array of conformations, but tend to favor native-like organization. (iii) Core modules have been covalently linked in an attempt to produce an N state, in which one conformation is substantially more stable than all other accessible conformations. (iv) Dynamics and structure of a BPTI mutant perturbed outside the core have been determined. Mutant G37A is destabilized by about 5 kcal/mol relative to WT, and is unusual in BPTI mutants in exhibiting rollover kinetics in denaturant-dependent chevron plots. Although G37A has the same average NMR structure as WT, it also has substantial increases in internal motion, indicated by hydrogen exchange rates and aromatic ring flips.
Structure and Dynamics of 6-Hydroxymethyl7, 8-dihydropterin Pyrophosphokinase
Maria L Zavodszky, Paul C. Sanschagrin, and Leslie A. Kuhn, Department of Biochemistry, Michigan State University, East Lansing, M148824. http://www.bch.msu.edu/labs/kuhn
It is widely accepted that flexibility is indispensable for protein function. One primary function of a protein is to recognize and bind other molecules. The question is how much flexibility is needed, in general, for protein-ligand interactions, and how this flexibility partitions between the protein and its ligand. Most algorithms designed to identify and dock ligands handle the proteins themselves as rigid bodies. Those that do take into account induced complementarity upon interaction use either side chain rotamer libraries or other sampling techniques and are too slow for use in molecular screening. Our screening program, SLIDE (Screening for Ligands by Induced-fit Docking Efficiently), models flexibility by allowing both protein side chain rotations and full ligand flexibility. Our starting assumption is that both the protein and the ligand change their conformation as little as possible upon binding to each other. SLIDE reduces the large number of ligand candidates to a manageable number using distance geometry techniques to compare inter-atomic distances and number of hydrogen bond donors and acceptors of each ligand with those in the template representing the binding site. Mean-field theory is used to select minimal directed rotations of bonds both in the ligand and the protein side chains to resolve interatomic collisions between the target and those ligands that have a complementary shape and chemistry. Each collisionfree ligand orientation is scored based on the number of hydrogen bonds and the hydrophobic complementarity with the protein. Results on screening for ligands to thrombin indicate that our assumption of minimal motion works well in this case.
Honggao YanI, Genbin Shi. i Jaroslaw Blaszczyk, 2 Bin Xiao, 2 and Xinhua Ji, 21Department of Biochemistry, Michigan State University, East Lansing, M148824 USA, 2Program in Structural Biology, National Cancer Institute, P.O. Box B, Frederick, MD 21702 USA
UPCOMING MEETINGS
6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate biosynthetic pathway. Folate cofactors are essential for life. Mammals derive folates from their diets, whereas most microorganisms must synthesize folates de novo. HPPK is therefore an ideal target for the development of novel antimicrobial agents. As a small (158 residues, ~ 18 kDa), stable, monomeric protein, E. coli HPPK is also an excellent model system for studying the mechanisms of enzymatic pyrophosphoryl transfer. The structures of apoHPPK and many complexes have been determined by x-ray crystallography and multidimensional multinuclear NMR spectroscopy. The structural studies have revealed not only the detailed interactions between the substrates and the enzymes but also dramatic,unusual conformational and dynamical changes upon binding the substrates or substrate analogs.
International Workshop on Methods for Macromolecular Modelling (M 3)
558
October 2 0 0 0
Courant Institute o f Mathematical Sciences N e w York, NY, USA October 12-14, 2000
The purpose of the multidisciplinary workshop is to bring together both developers of computational tools for biomolecular simulations and those biological and chemical scientists who use computer modelling to macromolecular problems. The workshop will be co-sponsored by Society for Industrial and Applied Mathematics.
.J. Mol. Graphics Mod., 2000, Vol. 18, August-October
Topics Long-term molecular dynamics simulations • Conformational sampling: equilibrium and nonequilibrium processes •
• Multiscale modelling • Quantum/classical mechanics • Fast electrostatics applications to DNA modelling, enzyme catalysis, and DNA/protein systems The program will provide an opportunity for scientific exchange among biomolecular researchers, computer scientists, and applied mathematicians. Applied mathematicians and computer scientists will benefit from direct interaction with the modelers, and biochemical modelers will be exposed to recent developments in numerics and algorithms from which their studies can benefit. The will stimulate and integrate ideas from disparate disciplines, educate young investigators interested in the field, and assess current progress as well as pinpoint future directions for the field through a Perspectives session at the end of the workshop. Articles by invited speakers will be collected in Springer Verlag's Lecture Notes series in Computational Science & Engineering (LNCSE), edited by members of the organizing committee.
Contact Dr. Tamar Schlick Courant Institute of Mathematical Sciences New York University 251 Mercer Street New York, NY 10012 Tel: 212-998-3116 Fax: 212-995-4152
workshop @biomath, nyu. edu http://monod, biomath, nyu. edu/-hgan/conf_O0, html
• Ken Dill, University Of California, San Francisco • Robert Fletterick, University Of California, San Francisco • Simon Kearsley, Merck • Peter Kollman, University Of California, San Francisco • Irwin Kuntz, University Of California, San Francisco • Jon Mason, Bristol-Myers Squibb • Ken Merz, Pharmacopeia • David Pearlman, Vertex Pharmaceuticals • Tom Scanlan, University Of California, San Francisco • Bruce Tidor, Massachus.etts Institute of Technology • Dennis Underwood, DuPont Pharmaceuticals • Gennady Verkhivker, Agouron • Jim Wells, Sunesis Pharmaceuticals
Contact Kristina Clarke University of California, San Francisco Department of Pharmaceutical Chemistry 513 Parnassus Avenue, Room S-926, San Francisco, CA 94143-0446 USA Tel: 415-514-0148 Fax: 415-502-4690 kristina @cgl. ucsf edu http://mdi.ucsf edu/
Computational Genomics October 26-31, 2000 Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724 USA
Drug Design and Discovery
Instructors
October 13-14, 2000 University of California, San Francisco Laurel Heights Conference Center 3333 California St. San Francisco, CA 94118 USA
• William Pearson, University of Virginia, Charlottesville • Randall Smith, SmithKiine Beecham Pharmaceuticals This course presents a comprehensive overview of the theory and practice of computational methods for gene identification and characterization from DNA sequence data. It focuses on approaches for extracting the maximum amount of information from protein and DNA sequence similarity through sequence database searches, statistical analysis, and multiple sequence alignment. Additional topics are gene recognition, exon/intron prediction, identifying signals in unaligned sequences, and integration of genetic and sequence information in biological databases. Lectures are combined with hands-on exercises; students are encouraged to use their own data. The course is designed for biologists seeking advanced training in biological sequence analysis, computational biology core resource directors and staff, and for scientists in other disciplines, such as computer science, who wish to survey current research problems in biological sequence analysis.
Topics • Drug Design and Discovery • Medicinal and Pharmaceutical Chemistry The meeting will provide many interesting perspectives on how the science and the technology of drug discovery are changing and will continue to change in the era of combinatorial chemistry and genomics. The meeting is sponsored by the Department of Pharmaceutical Chemistry and the Molecular Design Institute of the University of California, San Francisco. The meeting is chaired by Professors Peter Kollman, Ken Dill, and Irwin (Tack) Kuntz who have brought together an impressive group of speakers to describe challenges in using current technologies and needs and prospects for the future.
Speakers • Paul Anderson, Senior VP Chemical and Physical Sciences, DuPont Pharmaceuticals
• Johan Aqvist, Uppsala University • Fred Cohen, University Of California, San Francisco
Contact Course Registrar Cold Spring Harbor Laboratory Meetings & Courses Office 1 Bungtown Road Cold Spring Harbor, NY 11724 USA
J. Mol. Graphics Mod., 2000, Vol. 18, August-October
559
meetings @cshl. org http://nucleus, cshl. org/meetings/2OOOc-info, htm
November 2000
Ninth Conference on Current Trends in Computational Chemistry November 3-4, 2000 Vicksburg, Mississippi, USA This .symposium will cover all areas of computational chemistry as well as quantum chemistry.
Invited Speakers • • • • • • • • • • •
Benoit Champagne, University Notre-Dame de la Paix Jurgen Gauss, Mainz University Ilya Kaplan, University of Mexico Jerome Karle, Naval Research Laboratory Iwao Ohmine, Nagoya University Mark Olson, Biomedical Supercomputer Center Roman Osman, Mt. Sinai School of Medicine Michele Parrinello, Max-Planck Institute Andrzej Sadlej, Nicolaus Copernicus University at Torun Henry F. Schaefer III, University of Georgia Vladimir Spirko, Hejrovsky Institute of Physical Chemistry • Robert E. Wyatt, University of Texas at Austin • Tom Ziegler, University of Calgary
Contact Department of Chemistry, Jackson State University, Jackson, MS 39217 USA Conference Chairman: Jerzy Leszczynski, Tel: 601-979-3482
jerzy2, iris5.jsums, edu Conference Secretary: Ms. Shonda R. Allen, Tel: 601-979-3723 srallen @stallion.jsums, edu http://ccmsi, jsums.edu/cctcc/
• Juan Enriquez, Senior Researcher, Genomics, Harvard Business School, USA • John G. Sgouros, Head of Computational Genome Analysis Laboratory, Imperial Cancer Research Fund, London, UK • Klaus Lindpaintner, Director and Vice President, Roche Genetics (Europe), F. Hoffman La Roche, Switzerland
Contact www. ibc-biomics, corn
December 2000
6th Australian Molecular Modelling Workshop (MM2000) December 5-8, 2000 RMIT University Melbourne, Australia
Topics • • • •
Colloid and Surface Chemistry Drug Design and Discovery Medicinal and Pharmaceutical Chemistry Surfactants, Molecular Modelling, Genomics
Session Titles • • • • • • • • • •
First Principles Molecular Dynamics Non-equilibrium Molecular Dynamics Quantum Chemistry Atomistic Simulations of Solids Surfaces and Interfaces Polymer Modelling Drug Design Protein Modelling Genomic Analysis Bioinformatics
Contact
November 13-16, 2000 Messe Stuttgart International Stuttgart, Germany
Molecular Modelling Workshop Anjani Singh Department of Applied Physics RMIT, GPO Box 2476V Melbourne, Victoria 3001, Australia Tel: 61 3 9925 2600 Fax: 61 3 9925 5290
Topics
mm2000 @rmit. edu. au http://www.ph, rmit. edu. au/mm2000
Biomics
• Genomic and proteomic technology • Agrogenomics • New and exciting topics on structural biology and in silico biology • Bioinformatics • Applications • Licensing workshop
Speakers • Leroy Hood, President and Director, Institute for Systems Biology, USA • Denis Hochstrasser, Geneva Proteomics, Geneva, Switzerland
560
J. Mol. Graphics Mod., 2000, Vol. 18, August-October
Critical Assessment of Techniques for Free Energy Evaluation December 7-8, 2000 Asilomar Conference Center Asilomal; CA USA
Topics Biological Chemistry, techniques for predicting energies of binding and solvation CATFEE is a challenge and meeting designed to assess and discuss the techniques employed in computer assisted drug
design efforts. CATFEE will provide the opportunity to modelers and experimentalists to test new algorithms and evaluate established techniques used for the prediction of binding free energies.
January 2001
Contact
January 24-26, 2001 SwissOtel Zurich Am Marktplatz Oerlikon CH-8050 Zurich, Switzerland
CATFEE Tel: 323-995-6599 catfee @uqbat: ncifclf go v http://uqbar.ncifcrf gov/~catfee/
Gene Function Prediction GeneRAGE: Algorithm for Sequence Clustering and Domain Detection Dr Cristos Ouzounis, EB[
Structure-based Drug Design December 13-15, 2000 St. Catherine's College Oxford, UK
Automatic Discovery of Regulatory Patterns in Promoter Regions Based on Whole Cell Expression Data and Functional Annotation Dr. Steen Knudsen, Technical University of Denmark
Topics Computational Chemistry, Drug Design and Discovery
Target Gene Identification from Expression Array Data by Promoter Analysis Dr. TITomas Werner, Genomatix Software GmbH
Session Titles • • • • •
Integrative Bioinformatics High.Throughput Interpretation of Pathways and Biology
Principles and applications of structure based drug design Advances in computational methods Advances in experimental methods New drug targets Combinatorial Chemistry, Genomics and Proteomics
Combining Gene-Finding Programs to Increase Prediction Accuracy Dr. Cecilia Hammar, University of SkOvde (tentative) Functional Gene Networks: A Case Study of a Novel Data Management Approach for Bioinformatics Dr. Stephan Heymann, Kehnan Gesellschaft fiir Geninformation mbH
Contact Rebecca Wade The Molecular Graphics and Modelling Society, UK wade @embl-heidelbe rg. de h ttp://ww w.mgms. org/oxford2000/
Stability and Flexibility of Cellular Pathways Dr. Rajah Kumar, Sarnoff Corporation
Structural Genomics A Comprehensive Database of Protein Structure Models for Drug Discovery Dr. Tod M. Klingler, Prospect Genomics, Inc.
GRID 2000: International Workshop on Grid Computing in Conjunction with the 7th International Conference on High Performance Computing
The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli Dr. Sarah A. Teichmann, University College London
December 17-20, 2000 Bangalore, India
Topics Computational Chemistry, Grid Fabrics and Architectures
Sponsors • IEEE Computer Society • ACM SIGARCH GRID 2000 is an international meeting that brings together international grid computing researchers, developers, practitioners, and users. The aim of GRID 2000 is to serve as a forum to present current and future work as well as to exchange research ideas in this field.
Structural Pattern Localization Analysis by Sequential Histograms Speaker to Be Determined, IBM, T.J. Watson Research Center (tentative)
Visualizing Gene Expression Data Microarray Analysis as Module of LION's Integrated Life Science Informatic Platform Dr. Jan Michel, LION Bioscience AG A Decision Analytics Framework for Bioinformatics Dr Mark Demesmaeker, Spo~ire Inc. High-Throughput Research Using Microarray Gene Expression Information Dr. Frank A. White, InforMax, Inc.
Contact Rajkumar Buyya GRID Monash University Clayton Campus School of Computing Science and Software Engineering Melbourne, Australia
Gene Profiling for Target Identification New Bioinformatics Approaches in Functional Genomics Dr. Jean-Michel Claverie, CNRS
http://www, buyya, o rg/Grid2000/
Human Adult Skeletal Muscle Transcriptional Profile
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Reconstructed by Novel Computational Approach Prof. Gian Antonio Danieli, University of Padua
• Darren Green, GlaxoWellcome • lain Mclay, GlaxoWellcome • Dave Brown, Pfizer
Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation
Contact
Dr. Charles A. Mein, University of Cambridge (invited)
Dr. Darren Flower Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK Tel: +44 1635 577954 Fax: +44 1635 577954
Protein Expression
Proteins Have a Diverse and Distinct Repertoire of Interactions
Dr. Michael Lappe, European Bioinformatics Institute
darren.flower@jennerac, uk
Analysis of the Transcriptome by a Combined Approach
Dr. Alon Amit, Compugen
April 2001
Mining Mass Spectrometric Data for Disease Biomarkers
221th American Chemical Society (ACS) National Meeting
Dr. Pierre Huyn, SurroMed, Inc. Computational
Genomics
April 1-6, 2001 San Diego, CA USA
Genome-to-Genome Comparisons Using Terablast
Mr. Marry Gollery, TimeLogic, hw. Fast Probabilistic Analysis of Sequence Function Using Scoring Matrices
Contact American Chemical Society Meetings Department 1155 Sixteenth Street, N.W. Washington, DC 20036 USA Tel: 202-872-4396 Fax: 202-872-6128
Dr. Craig NeviU-Manning, Rutgers University (tentative) System for Integrating Data on GABA Receptors Dr. Hannah Hong Xue, The Hong Kong University of Science and Technology
[email protected]
Genomic Discoveries Quickly Converted into SmallMolecule Drug-Discovery Programs
Second Joint Sheffield Conference on Chemoinformatics: Computational Tools for Lead Discovery
Speaker to Be Determined, Iconix Pharmaceuticals, Inc.
Contact Christina Lingham 1037 Chestnut St. Newton Upper Falls, MA 02464 USA Tel: 617-630-1364 Fax: 617-630-1325
cling ham @healthtech, cam www.healthtech, com/2OO1/bne/index, htm
March 2001
Cutting Edge Approaches to Drug Design March 13, 2001 Scientific Societies Lecture Theatre Seville Row, London, UK This meeting addresses methods of drug design at the cutting edge: molecular simulation, knowledge management, and informatics. A key objective of the meeting is to explore how synergistic collaboration between informaticians and the experimental chemist can transform the speed and profitability of the pre-clinical pharmaceutical research process. The meeting is organized by the Royal Society of Chemistry through the Biological and Medicinal Chemistry Sector and Molecular Modelling Group.
April 9-11, 2001 Stephenson Hall University of Sheffield, UK The conference will cover all aspects of lead discovery including: • 3D databases, including docking and pharmacophore analysis • Assay QC and its influence on data mining • Chemical data mining • Descriptor validation • Design of leadlike combinatorial libraries • Design of screening collections • e-business to facilitate lead discovery • Novel software and hardware systems for lead discovery • Selective compound acquisition from in house and commercial suppliers • Similarity and clustering methods • Structure-activity methods for lead identification and early optimization • Structure-based design for lead identification and early optimization • Virtual screening • Case histories
Provisional Speakers List
Contact
• Prof. Sir Tom Blundell, FRS • Andy Lyall, Oxford GlycoSciences • Andy Davis, AstraZeneca
Val Gillet
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v.gillet @sheffield.ac, uk www.shef. ac. uk/cisrg/shef2001
Magnetic Resonance in Chemistry and Biology April 20-27, 2001 Zvenigorod Russian Federation The aim of the Xlth conference is to bring together scientists interested in the development of Magnetic Resonance techniques and experimental methods and their applications in chemical and biological research.
Session Titles • Nitric oxide in chemistry and biology • Advanced NMR imaging in biomedical fields • The environment and magnetic resonance research Contact Dr. Vladimir Sharygin
Institute of Chemical Physics of Russian Academy of Sciences Kosygin's Street 4 Moscow Russian Federation 117977
http ://www. chem.msu, su/eng/events/zveni gOl.html
July 2001 Intelligent Systems for Molecular Biology July 21-25, 2001 Copenhagen, Denmark Contact Johanne Keiding
johanne @cbs. dtu. dk
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