6th Joint Sheffield Conference on Chemoinformatics

22nd-24th July, 2013
Sheffield Peace Gardens Sheffield Winter Gardens Sheffield University Firth Hall The Edge Sheffield Botanical Gardens

Location, Travel &

Sponsors &

Conference Programme



TEA/COFFEE - Exhibition area (bar)
11:20-11:30 Conference Welcome: Val Gillet
Chair: Val Gillet
11:30-12:00 Damjan Krstajic, Research Centre for Cheminformatics
Common Mistakes in Building QSAR Models
Abstract Presentation
12:00-12:30 Robert D. Clark, Simulations Plus, Inc.
Estimating Classification Uncertainty for Ensemble Models
Abstract Presentation
12:30-14:00 SIT DOWN LUNCH - Dining Room, Ground Floor
Poster set-up for Poster Session I (posters 1-28)
  AFTERNOON SESSION A: Virtual Screening
Chair: Chistian Lemmen
14:00-14:30 Christos A Nicolaou, Eli Lilly and Company
The Lilly Reachable Chemical Space System: Bridging Chemical Synthesis Potential with Discovery Chemistry
Abstract Presentation
14:30-15:00 Lazaros Mavridis, University of St Andrews
Predicting Athletic Performance-enhancing Substances by Protein Target Prediction
Abstract Presentation
15:00-15:30 Lewis R. Vidler, Institute of Cancer Research
Correlation Between Virtual Screening (VS) Success and Druggability for Protein-Protein Interaction (PPI) Targets
15:30-16:00 TEA/COFFEE - Poster area and Exhibition area (bar)
Chair: Alexandre Varnek
16:00-16:30 Thierry Hanser, Lhasa Ltd
Self Organising Hypotheses Networks: A New QSAR Approach to Automatically Discover and Organize Knowledge
16:30-17:00 Rocco Varela, Certara
Surflex-QMOD: Physically Meaningful QSAR
17:00-18:30 MGMS AGM
Pre-dinner drinks
Buffet Supper
- Exhibition area (bar)
Drinks sponsored by the Royal Society of Chemistry - Chemical Information and Computer Applications Group
Poster session sponsored by the Journal of Cheminformatics


  MORNING SESSION A: Algorithmic Techniques I
Chair: Matthias Rarey
9:00-9:30 Tuomo Kalliokoski, Lead Discovery Center GmbH
SubCav - Tool for Subpocket Comparison and Alignment
Abstract Presentation
9:30-10:00 Nicola J Richmond, GlaxoSmithKline
Hierarchical Fuzzy Clustering with a Galois Lattice
10:00-10:30 Roger Sayle, NextMove Software
Extraction, Analysis, Atom Mapping, Classification and Naming of Reactions from Pharmaceutical ELNs.
Abstract Presentation
10:30-11:00 TEA/COFFEE - Poster area and Exhibition area (bar)
  MORNING SESSION B: Drug Discovery
Chair: Uta Lessel
11:00-11:30 Emanuele Carosati, University of Perugia
Modeling Structure-Metabolism Relationships: from the Human Cytochrome P450 Consortium Initiative a New Technology to Predict P450 Inhibition, Metabolic Stability and Isoform Selectivity
11:30-12:00 Cédric Merlot, Drugdesigntech SA
Integration of Network Biology and SAR Approaches for Early Safety Evaluation
12:00-12:30 Alexandre S. Lawrenson, The University of Liverpool
Targeting Isoprenoid Biosynthesis to Treat Human Malaria
Buffet Lunch
- Exhibition area (bar)
Poster set-up for Poster Session II (posters 29-55)
  AFTERNOON SESSION A: Algorithmic Techniques II
Chair: Jonathan Vessey
14:00-14:30 Andrew Dalke, Dalke Scientific
Varkony Revisited: Subgraph Enumeration and the Multiple MCS Problem
14:30-15:00 Guillermo Restrepo, Universidad de Pamplona
Looking for the Best QSAR and Docking Methods
Abstract Presentation
15:00-15:30 J. Willem M. Nissink, AstraZeneca
Tracking Compound and Project Progress Through Multi-objective-based Compound Quality Assessment
15:30-16:00 TEA/COFFEE - Poster area and Exhibition area (bar)
Poster session sponsored by the Journal of Cheminformatics
18:30 Coaches to Cutler's Hall
Sponsored by Chemical Computing Group
22:15 Coaches to Endcliffe Village


  MORNING SESSION A: Representation and Visualisation
Chair: Peter Ertl
9:00-9:30 Simon Grimshaw, Chemical Computing Group
Rationalization and Visualization of Non-bonded Interactions using Extended Hueckel Theory
9:30-10:00 Stefan Bietz, Center for Bioinformatics
Prediction of Tautomers and Protonation States in Protein-Ligand Binding Sites
10:00-10:30 Colin Batchelor, Royal Society of Chemistry
Validation and Standardization of Molecular Structures in General and Sugars in Particular: a Case Study
Abstract Presentation
10:30-11:00 TEA/COFFEE - Poster area and Exhibition area (bar)
  MORNING SESSION B: Database Analysis
Chair: Nicola Richmond
11:00-11:30 Pekka Tiikkainen, Merz Pharmaceuticals GmbH
Estimating Error Rates in Bioactivity Databases
Abstract Presentation
11:30-12:00 Ilenia Giangreco, AstraZeneca
A Challenging Dataset to Validate Pharmacophore Programs – Automated Protocol to Select and Overlay Structures from the RCSB Protein Data Bank.
Abstract Presentation
12:00-12:30 Bernd Beck, Boehringer Ingelheim Pharma GmbH & Co.KG
BioProfile - Extract Knowledge About Compound Cross Reactivities from Corporate Databases
Abstract Presentation
12:30-13:00 Paul J Kowalczyk, SCYNEXIS
Using Open Source Tools and Public Data to Build Machine Learning Models in Support of Neglected Diseases Drug Discovery
13:00-14:00 BUFFET LUNCH - Dining Room, Ground Floor

Poster Abstracts

Please note that poster boards will be Landscape - 1m high and 1.75m wide. These will require Velcro-tabs for mounting.


1 “Prediction Fingerprint”: A New Fingerprint for Virtual Screening Based on Class Predictions of Random Forests
Sereina Riniker, Gregory Landrum Abstract
2 A Multi-label Approach to Multi-Target Prediction.
M. Avid Afzal, Hamse Y. Mussa, Andreas Bender, Robert C. Glen Abstract
3 Similarity in the Context of the Orphan Drug Legislation
Pedro Franco, John Holliday, Peter Willett Abstract
4 Similarity Searching and Screening for Porous Materials
Richard Luis Martin, Maciej Haranczyk Abstract
5 Scaffold-Focused Virtual Screening to Identify Novel Kinase inhibitors
Sarah R. Langdon, Nathan Brown, Julian Blagg Abstract
6 Use of Finite Mixture Models for Clustering Chemical Compounds and Novelty Detection.
Damjan Krstajic, Simon Thomas Abstract
7 Chemical Patterns: A Visual Approach to Interpretation and Design
Karen Schomburg, Lars Wetzer, Matthias Rarey (presenting) Abstract
8 A novel approach to De Novo design utilising Reaction Networks
James E. A. Wallace, Beining Chen, Michael J. Bodkin, Val J. Gillet Abstract
9 Construction and Use of a Fragment Virtual Screening Library
Richard Hall Abstract
10 In Silico Structure-Based Drug Design (SBDD) on S100P: Identification of a lead compound towards a therapeutic intervention in pancreatic cancer
Ramatoulie Camara, Sharon Rossiter, Vishal Kholi, Stewart B. Kirton Abstract
11 Highly Soluble/Poorly Metabolized BDDCS Class 3 Drugs Share High Similarity with Small Peptides
Fabio Broccatelli, Nathan Brown, Cristian G. Bologa, Jeremy J. Yang, Tudor I. Oprea Abstract
12 Design, Synthesis and Biological Testing of New Antimalarial Drug Candidates
Robert D. Clark, Michael S. Lawless, Walter S. Woltosz Abstract
13 High-Throughput Screening Case Studies for the Successful Identification of Ion Channel Ligands
Alexander Böcker, Pierre Ilouga, Sabine Schaertl, Insa Winzenborg, Stephen Hess, Annett Müller Abstract
14 Algorithms for Automatic Tautomer Generation and Their Applications
Nikolay T. Kochev, Vesselina H. Paskaleva, Nina Jeliazkova Abstract
15 A Novel Drug for Uncomplicated Malaria: Chemoinformatic Compound Selection and QSAR Towards an Optimised Lead
Neil G. Berry, Raman Sharma, Alexandre S. Lawrenson, Paul M. O'Neill, Steve A. Ward, Giancarlo A. Biagini, Nick Fisher, Serge Parel Abstract
16 Experimental Validation of In Silico Target Predictions Onsynergistic Protein Targets
Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Robert C. Glen, Adrian Velazquez-Campoy, Andreas Bender Abstract
17 inSARa: Enabling Intuitive and Interactive (Large-Scale) SAR Analysis by Reduced Graphs and Hierarchical MCS-based Network Navigation
Sabrina Wollenhaupt, Knut Baumann Abstract
18 Identification of (Latent) Hit Series in Primary Screening Data
Ansgar Schuffenhauer, Thibault Varin, Marie-Cecile Didiot, Christian N. Parker Abstract
19 CONFECT: Generating Conformations from an Expert Collection of Torsion Patterns
Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey Abstract
20 Scaffold Hopping for Aromatic Rings. Can MM Compete with QM?
Sree Vadlamudi, Tim Cheeseright, Martin Slater, Mark Mackey Abstract
21 Ligand-Based Virtual Screening and Visualization in the SMILES Chemical Space
Julian Schwartz, Jean-Louis Reymond Abstract
22 Macromolecules or Big Small-Molecules? Handling Biopolymers in a Chemical Registry System
Noel M O'Boyle, Evan Bolton, Roger A Sayle Abstract
23 Working Life Science Data on the Web: A New Approach Driven by Users and Processes
András Strácz, Iván Solt, Gábor Guta, Anna Tomin Abstract
24 Prediction of Thermal Properties of Organic Peroxides Using QSPR Models
Vinca Prana, Patricia Rotureau, Guillaume Fayet, Carlo Adamo Abstract
25 Interpretation of Statistical Machine Learning Models for Ames Mutagenicity
Samuel Webb, Thierry Hanser, Brendan Howlin, Paul Krause, Jonathan Vessey Abstract
26 Molecular Dynamics Simulation of Bicyclic Peptides
Xian Jin, Julian Schwartz, Prof. Dr. Jean-Louis Reymond Abstract
27 OPSIN: Taming the Jungle of IUPAC Chemical Nomenclature
Daniel M. Lowe, Peter Murray-Rust, Robert C. Glen Abstract
28 LiSIs: An Online Scientific Workflow System for Life Sciences Research
C. C. Kannas, K. G. Achilleos, Z. Antoniou, C. A. Nicolaou, C. S. Pattichis, I. Kalvari, I. Kirmitzoglou, V. J. Promponas Abstract


29 Dealing with Combinatorial Chemical Space: Towards a Universal Framework
Florian Lauck, Matthias Rarey Abstract
30 Predicting pKa Values from EEM Atomic Charges
Stanislav Geidl, Radka Svobodová Varekova, Crina-Maria Ionescu, Ondrej Skrehota, Tomas Bouchal, David Sehnal, Jaroslav Koca Abstract
31 The MQN-Mapplet: Interactive Access to Millions of Molecules on your Desktop
Mahendra Awale, Ruud van Deursen, Jean-Louis Reymond Abstract
32 Making the Most of Approximate Maximum Common Substructure Search
Péter Englert, Péter Kovács Abstract
33 The FPS Format and the Chemfp Package
Andrew Dalke Abstract
34 Virtual Screening to Identify Novel Antimalarial Chemotypes
Alexandre S. Lawrenson, Neil G. Berry, Raman Sharma, Paul M. O’Neill, Steve A. Ward, Giancarlo A. Biagini, Nick Fisher, Alison E. Shone Abstract
35 An Extended Analysis on Turbo Similarity Searching
Alia-Azleen Zainal, Norasyikin Yusri, Yong Pei Chia, Nurul Malim, Shereena M Arif Abstract
36 Beating (the) Competition in Lead Discovery; Property and Structural trends in Allosteric Regulators
Gerard JP van Westen, Anna Gaulton, John P Overington Abstract
37 Modeling Species Selectivity in Rat and Human Cytochrome P450 2D Enzymes
Grace Edmund, Brendan Howlin, Dave Lewis Abstract
38 Chemical Landscape Analysis – the Case of Tautomers
Nina Jeliazkova, Nikolay T. Kochev, Vedrin Jeliazkov Abstract
39 Accelerating Data Fusion using High Performance Computing (Multi-core Processors and Graphics Processing Unit)
Mohd-Norhadri Hilmi, Mostafa AlBarmawi, Nurul Malim, Nur'aini Abd Rashid, Shereena M Arif Abstract
40 Building of 3D Structure Model and Annotation of Bifidobacterial Beta-galactosidase
Vladimir Vukic, Dajana Hrnjez, Spasenija Milanovic, Mirela Ilicic, Katarina Kanuric Abstract
41 VHELIBS, a Validation Helper for Ligands and Binding Sites
Adrià Cereto Massagué Abstract
42 Visually Interpretable Analysis of Kinase Selectivity Related Features Derived from Field-based Proteochemometrics
Vigneshwari Subramanian, Peteris Prusis, Lars-Olof Pietilä, Henri Xhaard, Gerd Wohlfahrt Abstract
43 Optimizing Chemical Information Workflows by Integrating Reaxys
Sebastian Radestock Abstract
44 Virtual Screening for Sirtuin Inhibitors using Target-specific Docking Methods.
Michael Scharfe, Martin Pippel, Benjamin Maurer, Manfred Jung, Wolfgang Sippl Abstract
45 Computer Modelling of Synergistic Effects in Intestinal P-Glycoprotein Transport and Cytochrome P450 3A4 Metabolism
Alison Choy, Andrew Howlett, Johannes Kirchmair, Robert Glen Abstract
46 Comparison of Similarity Coefficients for Ligand-based Virtual Screening using Binary and Weighted Fingerprints
Hua Xiang, John Holliday, Peter Willett Abstract
47 Ligand Based Virtual Screening using Ensemble Classification for the Identification of Anti-Tubercular Molecules
Nisha Chandran, Anurag Passi, Abhilash Gangadharan, OSDD Consortium Abstract
48 Flavivirus Fusion Inhibitors: Identification and Putative Mechanism of Action
Evgenia V. Dueva, Dmitry I. Osolodkin, Liubov I. Kozlovskaya, Victor V. Dotsenko, Vladimir M. Pentkovski, Vladimir A. Palyulin, Galina G. Karganova, Nikolay S. Zefirov Abstract
49 GTM-based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System
Héléna A. Gaspar, Gilles Marcou, Philippe Vayer, Alexandre Varnek Abstract
50 Commercial Fragment Coverage of Exemplified Medicinal Chemistry Substructures from ChEMBL
Yi Mok, Ruth Brenk, Nathan Brown Abstract
51 Virtual Screening on Billions of Small Molecules from the Chemical Universe Database GDB-17
Lars Ruddigkeit, Lorenz C. Blum, Jean-Louis Reymond Abstract
52 The Origins of 3D Shape in Drug-Like Molecules
Nicholas C. Firth, Nathan Brown, Julian Blagg Abstract
53 Target Identification of Anti-prion Compounds
Valencia, J.M., Chen, B., Gillet, V.J. Abstract
54 Practical Application of Selected Computational Methods for Prediction of Xenobiotic Metabolism: Rational Strategies for Use
Przemyslaw Piechota, Mark T. D. Cronin, Mark Hewitt, Judith C. Madden Abstract
55 Regulatory Mechanisms and Pharmacological Control of Epileptic Seizures in Zebrafish
Simon Hand, Val Gillet, Joseph Harrity, Vincent Cunliffe Abstract

Student Bursaries

Thanks to the generosity of the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society we have been able to offer several student bursaries to cover the full registration costs (but not travel). All bursary awards have now been allocated.