We have now opened up the new release of seminar and discussion materials in the Program area of the eCheminfo web site at http://echeminfo.colayer.net/ including new materials from the Autumn InterAction meetings.
Please note that further release of materials from 2005 will be forthcoming in subsequent releases and that all 2003 and 2004 seminars are in the process of being moved to the Program areas, so watch out for further news releases here.
List of eCheminfo Seminars currently available in Program areas for Drug Discovery Innovation, Proteins, Screening, Web Services, Quantum Biochemistry, Graph Mining and the current Poster Session:
Drug Discovery Innovation
Structure-Based Design of Allosteric Protein Kinase Inhibitors, Jeff Wiseman (Locus Pharmaceuticals)
An Interactive Environment for Multiparameter Optimization, James H Wikel (Coalesix)
Computational Models are Needed to Make Drugs Safer and More Effective, G. Scott Lett (Bioanalytics Group)
Metabolomics for White Biotechnology, Lars M. Blank (University of Dortmund and the Institute for Analytical Sciences (ISAS), Dortmund )
Analysis Based on Molecular Diversity, Steve Boyer (IBM)
Is there any Sense in the Semantic Web?, Jim Cook (Volutio)
Proteins
Amyloid beta-protein oligomerization and Alzheimer’s disease, David Teplow (David Geffen School of Medicine at UCLA)
Direct observation of protein folding, misfolding and prion-like conformational infectivity, Feng Ding (University of North Carolina)
Detection of Intermediate States of Cell Adhesion Proteins Using Discrete Molecular Dynamics (DMD) Simulations Constrained By Nuclear Magnetic Resonance (NMR) Hydrogen Exchange (HX) Data, Richard Dixon (University of North Carolina)
All-atom protein folding with stochastic optimization methods, Wolfgang Wenzel (University of Karslruhe)
Folding@Home: Using worldwide desktop grid computing to break fundamental
barriers in molecular simulation, Vijay Pande (Stanford University)
Design of a folding inhibitor of the HIV-1 Protease, Guido Tiana (University of Milano)
Simulations of peptide inhibitors of Amyloid-beta fibrillogenesis, Joan-Emma Shea (University of California, Santa Barbara)
Folding and aggregation: A physics-based all-atom modeling, Yong Duan (University of California Davis)
Application of discrete molecular dynamics to protein folding and aggregation, Sergey Buldyrev (Yeshiva University)
Dewetting in nanoscale hydrophobic plates collapse and multi-domain protein folding, Ruhong Zhou (IBM)
Automated Methods for identifying Structural Motifs: Helix Couples in the Globins, Marc Fasnacht (Columbia University)
Reconstructing evasive protein states using NMR and molecular modeling: the Focal Adhesion Kinase story, Nikolay V. Dokholyan (University of North Carolina)
Protein modelling: simulating the thermodynamics and kinetics of protein folding, Jed Pitera (IBM)
Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family, Peter Winn (EMBL, Heidelberg)
Screening
Molecular Docking as a Virtual Screening Tool, Renee DesJarlais (Johnson & Johnson Pharmaceutical Research & Development, LLC)
Exploiting protein-specific information in docking, Willem Nissink (Cambridge Crystallographic Data Centre)
You can't find what's not there: the importance and the pitfalls of multiple representations of molecules in dockable databases, John Irwin (UCSF)
Pattern Recognition and Grid Computing in Drug Discovery, Graham Richards (University of Oxford)
The Issue of Protein Flexibility in Docking-Based Virtual Screening, Xavier Barril (Vernalis)
Beyond ligand flexibility: improvement and validation of rDock for Structure-Based Drug Design, David Morley (Enspiral Discovery Ltd)
Structure-based identification of GPCR ligands by high-throughput docking, Didier Rognan (University of Strasbourg)
Web Services
A Web-based Chemoinformatics System for Drug Discovery, Brett Tounge (Johnson & Johnson Pharmaceutical Research & Development, LLC)
Web enabling technology for the design, enumeration, optimization and tracking of compound libraries, Brad Feuston (Merck)
ZINC web services - providing 3D structures of purchasable compounds for virtual screening to humans and machines, John Irwin (UCSF)
Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web, Dimitris Dimitropoulos (European Bioinformatics Institute)
The Representation of Chemical Structures and its Application to Property Prediction, Johann Gasteiger (Universitaet Erlangen-Nuernberg)
Open Archives as a Route for the Capture, Dissemination and Access to Chemical Information, Simon Coles (University of Southampton)
Identification of biological units in protein crystals, Eugene Krissinel (European Bioinformatics Institute)
Upstream analysis of gene expression data: Reasoning microarray experiments, Alexander Kel (BIOBASE GmbH)
A Web Interface to Neural Network Prediction of 1H NMR Chemical Shifts, Joao Aires de Sousa (Universidade Nova de Lisboa)
Molecular similarity searching via a freely accessible web interface using the MOLPRINT 2D approach, Andreas Bender (Cambridge University)
Computer-aided prediction of biological activity spectra as a way to creating new effective and safe medicines, Vladimir Poroikov (Institute of Biomedical Chemistry of Rus. Acad. Med. Sci.)
MSDmotif: A Database Search and Retrieval System for the Analysis and Viewing of Protein Structure Motifs, Adel Golovin (EBI)
Quantum Biochemistry
Use of Quantum Mechanics in the Process of Drug Discovery, Ramkumar Rajamani (Bristol-Myers Squibb)
Semiempirical Comparative Binding Energy Analysis (SE- COMBINE) of a series of Trypsin Inhibitors, Martin Peters (Penn State)
On the art of computing of the Infra Red Spectra of molecules in the condensed phase, Paul Tavan (University of Munich)
Applications in Computational Quantum Biochemistry, Alessandro Curioni (IBM Zurich)
Kinetic isotope effects for enzyme-catalysed methyl transfer, Ian Williams (University of Bath)
Determination of the protonation states of the key aspartates in β-Secretase through QM/MM X-ray structure refinement, Ning Yu (Pennsylvania State University)
Computational Studies of Protein-Ligand and Protein-Solvent Interactions, Kaushik Raha (UCSF)
Quantum Mechanics for Drug Discovery, Lance Westerhoff & Ken Merz (QuantumBio)
Analysing enzyme activity and specificity by QM/MM modelling, Adrian Mulholland (University of Bristol)
Simulations of phosphoryl transfer reactions using new hybrid quantum mechanical/molecular mechanical methods, Darrin York (University of Minnesota)
Towards quantum mechanical force fields for biomolecules, Richard Bryce (University of Manchester)
The application of QM/MM techniques to model enzyme mechanisms and protein-ligand interactions, Harald Lanig (Erlangen University)
Graph Mining
Lazy-Structure-Activity-Relationships (lazar) for the in-silico Prediction of Chemical Carcinogenicity, Christoph Helma (University of Freiburg)
Graph-Theoretic Procedures for Searching Databases of Molecular Structures, Peter Willett (University of Sheffield)
Finding Discriminative Substructures Using Elaborate Chemical Representation, Joost N. Kok (Leiden University)
Alignment-free Potential Pharmacophore-Point Descriptors for "Informed" Similarity Searching, Gisbert Schneider (Johann Wolfgang Goethe-University)
Comparing Molecule Similarity Codings - Vectorial versus Structural Coding for ADME/Tox Prediction, Joerg Kurt Wegner (Tibotec BVBA)
Posters:
FlexScreen: Docking with Receptor Flexibility
B. Fischer, H. Merlitz, W. Wenzel, Forschungszentrum Karlsruhe, Germany
Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web
Dimitris Dimitropoulos, European Bioinformatics Institute, UK
The e-Malaria Project: Tools for Schools - An interactive computer aided drug discovery
Robert Gledhill, Sarah Kent, Jonathon Essex and Jeremy G. Frey*, School of Chemistry, University of Southampton, UK
Studying the long-range structure of flexible peptides by small-angle X-ray scattering and molecular dynamics
Bojan Zagrovic (1)*, Jan Lipfert (2), Guha Jayachandran (3), Eric J. Sorin (3), Ian S. Millett (3), Wilfred F. van Gunsteren (1), Sebastian Donaich (2) & Vijay S. Pande (3)
(1) Physical Chemistry Institute, ETH, Zurich, Switzerland
(2) Department of Physics, Stanford University, USA
(3) Department of Chemistry, Stanford University, USA
In silico Characterization of Stickler Syndrome Causing Human Collagen Proteins
K. Sivakumar (1), S. Balaji (1) and G. Radhakrishnan (2);
(1) Department of Chemistry, Sri Chandrasekharendra Saraswathi Viswa MahaVidyalaya (Deemed University), Enathur, Kanchipuram 631 561, Tamilnadu, India
(2) EXCEL and Polymer Science Labs, Central Leather Research Institute, Adyar, Chennai 600 020, Tamilnadu, India
Reducing the Synthetic Burdens of Lead Structure Optimization: A Novel Software-Aided Approach
Karim Kassam, Ryan Sasaki, and Michel Hachey, Advanced Chemistry Development, Inc., 110 Yonge Street, 14th Floor, Toronto, Ontario, M5C1T4 Canada
Improving Enrichment with eHiT’s Scoring Function Training Utility
Darryl Reid, Zsolt Zsoldos, Aniko Simon, and Peter Johnson, SimBioSys Inc. Canada
Open Babel and the Blue Obelisk, Open Standards and Open Software in Chemistry
Geoffrey Hutchison, Cornell University, Ithaca, NY, USA
Barry Hardy
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