 
EuroCUP V (2011)
Maximal Use of Information
•Hans Matter, Sanofi-Aventis,
Germany - "Development and Application of
Tailored Scoring Functions for
Protein-ligand Interactions" Download
•Brian Kelley,
OpenEye - "The Curate's receptor - pose
prediction using the good bits"
Download
•Terry Stouch, Science For
Solutions, USA - "The Intricacies of
Pharmaceutical Data: What Is Required to
Properly Understand it"
Download
•Krisztina
Boda, OpenEye - "The art of chemistry:
visualizing chemical information"
Download
•Nick Barton, GlaxoSmithKline, UK -
"Should we leave chemists to their own
devices?" Download
•Jurgen Bajorath, University of
Bonn, Germany - "Methods for SAR
Visualization" Download
Speed and
molecular calculation
•Brian Cole, OpenEye - "Higher
dimensional beliefs" Download
•David Leahy, Molplex, UK - "Most
Drug Discovery Scientists Could Be
Replaced by Software Systems"
Download
Precision
in molecular calculation
•Sally Price, University College
London, UK - "Progress and challenges in
the computational prediction of organic
crystal structures"
Download
•Andrew Grant,
AstraZeneca, UK - "What can we learn if we
actually compare theory to experiment?
Lessons from small molecule dipole
moments"
Download
•Osamu Ichihara,
Evotec, UK - "Characterizing Binding Site
Waters Using SZMAP, MD and FMO QM Methods"
Download
•Jens Nielsen,
Novozymes, Denmark - "Predicting protein
pKa values: what we can and cannot do"
Download
CUP XII (2011)
"Experimental
data that theorists could and should
use"
•Mike Doyle, Bristol
Myers Squibb, "Calorimetric Measurement
Ligand-Binding Thermodynamics and Coupled
Protonation Reactions" Download
“Theorists
who calculate things experimentalists
might want to measure”
•Christopher Bayly,
OpenEye, "Rapid estimation of Molecular
Entropy - a useful quantity?" Download
•Kennie Merz,
Quantum Theory Project, U. Florida., "A
little Experimental Information Goes a
Long Way to Making Things Right"
Download
“Predictive
methods beyond
discovery”
•Matthew Segall,
Optibrium, "Guiding the design of high
quality compounds in drug discovery"
Download
•Tony Slater,
pKaData Ltd, "Uses and abuses of
experimental pKa data" Download
“Myths
of Modeling”
•Helen Berman,
Rutgers U., RCSB, "Effective uses of the
Protein Data Bank: the do's and the
don'ts" Download
Shape
and electrostatics in
modeling”
•Ben Ellingson,
OpenEye, “Comparison of
pattern-based and algorithm-based
approaches to tautomer informatics”
Download
Mini-session
on "Discrete Water Modeling with
SZMAP"
•Anthony Nicholls, OpenEye, "An
introduction to semi-continuum modeling"
Download
•Demetri Moustakas,
AstraZeneca, "Flushing the molecular pipes
with SZMAP: a study of the aquaporin
selectivity filter" Download
Shape and
Electrostatics Session
•Frederico Nardi Sanofi-Aventis,
France - Topological Reshuffling: a
Geometrically Rationalized "Me Too"
Approach. Download
•Peter Taylor AstraZeneca (retired),
UK - Triage for Tautomers: from Casualties
to Computation. Download
•Paul Hawkins
OpenEye, USA - EON: I Cannot Tell You What
It Is, You Have to See It For Yourself.
Download
Are
Proteins Useful for Drug
Discovery?
•Mike Word OpenEye, USA - When Is PB
Wrong and What Can We Do About It?
Download
•Oliver Korb CCDC,
UK - Ensemble Docking Revisited
Download
Ligand-based
Modeling Rules
•Hugo Kubinyi BASF and University of
Heidelberg (retired), Germany - Scaffold
Hopping - A Successful Design Strategy.
Download
•Jonas Boström
AstraZeneca, Sweden - Exploiting the
Amazon.com Feature "People Who
Bought...Also Bought..." in Reagent
Selection. Download
•Jürgen
Bajorath University of Bonn, Germany -
Extracting SAR Rules from Compound Data.
Download
CUP XI (2010)
Evaluations of what the current
state-of-the-art can and can't
calculate
•Anthony Nicholls, OpenEye -
Perspective: Electrostatics: Why I keep
bothering. Download
•Matt Geballe, OpenEye - SAMPL2, the
beat goes on...Download
•Mike Word, OpenEye
- What’s Szmappening? Download
Fragment-based
Drug Discovery: Primary tool or tactic of
last
resort?
What and
when is the appropriate use of
FBDD?
•Anthony Nicholls, OpenEye -
Perspective: Information content and
fragments Download
•Philip Hajduk,
Abbott - Fragmented
Thinking...Download
It
doesn't matter how good your work is if
the chemists ignore it.
•Stephen Johnson, Bristol-Meyers
Squibb - We don’t make widgets: a
quest for relevant performance metrics in
CADD Download
•Dan Ortwine,
Genentech - Shaping Chemists' Expectations
Toward Modeling (and Modelers) - and Vice
Versa Download
•Youssef Bennani,
Vertex - Meddling with Modeling
Download
MMPB:
Panacea, useful or useless?
Some
rely on it, some find it useful and some
can't get anything out of it at all. Some
leading lights will be asked to give their
opinion.
•Anthony Nicholls, OpenEye -
Perspective: A little Physics is a
dangerous thing Download
•Richard Dixon,
Vertex - What is this usefulness you speak
of? Download
Statistical
Reasoning in Molecular Modeling and Ligand
Design
How best to use the information we have,
whether from ligands, proteins or
literature
•Anthony Nicholls, OpenEye -
Perspective: Ligands and information
content Download
New
technology and old dogs
Workflows, GPU's and clouds,
oh my!
•Anthony
Nicholls, OpenEye- Perspective: Old dogs
don't need new tricks, we need old ones
Download
•Bob Tolbert, OpenEye -
Polyglot Programming with the OpenEye
Toolkits
Download
•Brian Cole,
OpenEye-GPUs: What is all the fuss about?
Download
•Imran Haque,
Stanford-LINGOs & GPUs
Download
EuroCUP III
(2009)
Shape
& Electrostatics
•ROCS and the ROCS Query Editor, Bob
Tolbert, OpenEye Download
•Shape Descriptors: Sometimes Better
than Nothing, Brian Kelley, OpenEye
Download
•Shaping the Future
of in silico Drug Design: Accurate
Small-molecule Conformations from
Experiment, Andrew Almond, ConformetrixLtd
Download
Fragment
Design: Good Idea or the Latest Blind
Alley?
•Challenges in Fragment-based
Discovery, Roderick Hubbard, Vernalis
Download
•Pharmacophore
Development and NMR Validation of Small
Fragments as Novel Heparanase Inhibitors,
Rafael Gozalbes, CIPF Download
•Fragment-based
Design: a Promising Strategy, Hugo
Kubinyi, BASF Download
QSAR: Is
it Worth it?
•Descriptor-based Modeling of Ligand
Binding-An Illusion?
Dragos
Horvath, University of Strasbourg
Download
•AFMoCcon:
Incorporating Ligand and Receptor
Conformational Variability into
Tailor-made Scoring Functions, Holger
Gohlke, Univ. of Düsseldorf
Download
Databases
and Data Sources for Molecular
Modeling
•Marginally Less Bad Than the Rest,
Greg Warren, OpenEye Download
•Crystal Contacts
and Ligand Binding: Implications for
Scoring Functions, Jens Erik Nielsen,
University College Dublin Download
•The Conversion of
IUPAC's Compilations of pKas of Organic
Acids and Bases into
Substructure-searchable data, Tony Slater,
pKaData Ltd Download
CUP X (2009)
Shape
•Shape, Pose Prediction and the
American Way, Scott Brown, Abbott
Download
•Shape diversity in
fragment library design, Ken Brameld,
Roche Download
•View of an outsider
from the inside: Ligand treatment by the
PDB, Terry Stouch, RCSB Download
•Pre-computed 3D
similarity of small molecules: PubChem
3D!, Evan Bolton, NCBI Download
•Why is Quantum
Mechanics not more useful?, Tom Darden,
OpenEye Download
•The Levinthal Classic, Michael
Sherman, Stanford Download
•Docking - the Next 10 Years, Tack
Kuntz, UCSF Download
•Lies, Damned Lies, and
Molecular Modeling: It's Almost Always
Worse Thann You
Think, Steve
Muchmore, Abbott
•Much Ado About
Quantum Mechanics, Kennie Merz, QTP,
University of Florida Download
Electrostatics
•Considerations of small molecule
strain energy, Johannes Hermann, Roche
Download
•Entropy in
simulation & calorimetry, Demetri
Moustakis, AstraZeneca Download
•What did we learn
about solvation energies from SAMPL-1?,
Peter Guthrie, U. Western Ontario
Download
•Montreal or Bust:
SAMPL2, Geoff Skillman, OpenEye; Tom Peat,
Janet Newman CSIRO, Melbourne Download
Talk1
Talk2
•Electronic
polarization from the internal continuum:
an EPIC journey through the dielectric
jungle, Jean-Francois Truchon, Merck
Frosst Download
•Conformational
dependent partial charges and why a
dielectric might be your friend, Anthony
Nicholls, OpenEye Download
•What, oh what (if
anything) are we going to do about force
fields, Chris Bayly, Merck Frosst; Anthony
Nicholls, OpenEye Download
EuroCUP
II (2008)
Shape
& Electrostatics
•Conformers: the Sine Qua Non of
Shape, Paul Hawkins, OpenEye Download
•Taming the Hydroxyl Rotor, Roger
Sayle, OpenEye Download
Lead
Optimization & Structure-based
Design
•On the Impact of Virtual Screening
in Genuine Lead Generation Campaigns,
Stefan Schmitt, AstraZeneca Download
•The Effects of
Structural Changes on Molecular
Properties: Matched Molecular Pair
Analysis as a Tool for Lead Optimisation,
Andrew Leach, AstraZeneca Download
•Dirt Squad! -
Confessions of an AgroScientist, John
Delaney, Syngenta Download
Prospective
Science
•SAMPL Reprise: Nostradamus, Bohr,
Weathermen & Us, Geoff Skillman,
OpenEye Download
•A decade of blind
tests of crystal structure prediction:
organisation, outcomes and future, Graeme
Day, University of Cambridge Download
•Castalian
Allocution: Living in Castalia - The
Pitfalls in 'Rational' Design, Hugo
Kubinyi, BASF and University of Heidelberg
(retired) Download
Physical
Property Prediction
•A Survey of Halogens: Dummkopf,
Where Have You Put the Lone Pairs?, Peter
Kenny, AstraZeneca Download
•Unveiling the Janus
Face of Organic Fluorine, Holger Gohlke,
J.W. Geothe-University Download
•Halogens,
Smalogens: the Electrostatics of Awkward
Compounds, Anthony Nicholls, OpenEye
Download
•Prediction of
Aqueous Solubility in the Early Drug
Discovery Phase, Bernd Beck,
Boehringer-Ingelheim Download
CUP
IX (2008)
Shape
& Electrostatics
•Mathematics, Shape Space and Other
Marriages Made in Heaven, Paul Hawkins,
OpenEye Download
•PubChem3D: Relative
Diversity of Shape (and Colour), Evan
Bolton, NLM Download
•Field of Extremes:
If You Re-refine it, They Will Come, Greg
Warren, OpenEye Manuel Perola, Vertex
Download
Lead
Optimization Techniques.
Evaluations
•Drug Guru: A Computational Tool
that Uses Structural Transformations, Kent
Stewart, Abbott Laboratories Download
•SAMPL 1 at First
Glance, Geoff Skillman OpenEye
Download
•2D Control:
Emulating the Algorithms Inside Chemists'
Heads, Roger Sayle, OpenEye Download
EuroCUP
I (2007)
Chemical
information and modeling
•Virtual Exploration of Chemical
Space by Database Generation, Jean-Louis
Reymond, University of Berne Download
Structural
information
Structure and Property Predictions for
Molecular Organic Molecules:
•Progress and Blind Tests , Graemer
Day, University of Cambridge Download
•Computed Crystal
Energy Landscapes for the Prediction and
Understanding of Polymorphism, Sally
Price, University College London
Download
•Validating Crystallographic
Ligands, Brian Kelley,
OpenEye
Download
Electrostatics
•"Physically Correct Charges. Think
You Use Them? Think Again., Anthony
Nicholls, OpenEye Download
CUPVII
(2006)
Bioisosteres
•Re-defining bio-isosterism using
Rocs and Eon, Mike Tennant, Pharmix and
Andy Jennings, Takeda Download
•Bioisoelektrofigosteres: Beyond
what chemists already know? Geoff
Skillman, OpenEye Download
•Electrostatic
similarity Anthony Nicholls, OpenEye
Download
•Training: Docking
with Fred tutorial Paul Hawkins, OpenEye
Download
Talk1
Download
Talk2
Ligand
Design
•Similarity of Molecular Surfaces:
Tales of Multiple Scales Ajay Jain, UCSF
Download
•Integrating Virtual
Screening Technologies (VST) with
High-Throughput Screening (HTS): Some
Practical Examples, Tudor Oprea, UNM
Download
•A comparison of
structure-based and shape-based tools in
virtual screening Paul Hawkins,
OpenEye Download
Simulations
and Force Fields
•Your Tax Dollars at Work --
SimTK.org, really good free software for
physics-based simulation of biological
structures Michael Sherman,
Stanford
•Training: OEChem
examples Jeremy Yang, OpenEye Download
Structural
Biology
•Protein electrostatics Anthony
Nicholls Download
•An alternative
approach for the evaluation of docking
performance: RMSD vs. RSR, Stefan Schmitt,
AstraZeneca Download
CUP
VI (2005)
•Similar Ligands
Bind in a Similar Fashion Jönas
Bostrom, AstraZeneca Download
•Searching Libraries
and Searching Patents
HTML John Barnard,
Barnard Chemical Information,
Ltd.
•A Protein Crystallographer's
Perspective: Why Our Structures Aren't
Perfect and What We Can Do about It
Tom Transue, NIEHS, NIH Download
•A modest proposal on Virtual
Screening: We hold these truths to be
self-evident Glen Kellogg, Virginia
Commonwealth University Download
•e-preview: Searching US Patent Data
for Chemical Structures , Jim Cooper, IBM
Download
•Pharmacophore
Searching with OEChem Greg Bakken, Pfizer
Download
•A Genetic Algorithm
for Pharmacophore Elucidation Gareth
Jones, Arena Pharmaceuticals Download
CUP
IV (2003)
Proteins
•Andrews Binding Energy: Can it be
revisited? Tudor Oprea, U. New Mexico
Download
Electrostatics
•Prediction of Hydrogen-bond
strengths Peter Kenny, AstraZeneca
Download
•GBSA and other bad
theories of electrostatics, Anthony
Nicholls Download
•Perfect, Efficient and Most
Excellent Charges Roger Sayle Download
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