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PDB Ligands: Analysing their Structure & Binding Data |
InterAction Meeting Session, Bryn Mawr, Philadelphia, USA
Thursday 16 and Friday 17 October 2008
chaired by Marc Nicklaus (National Institutes of Health) Bio....
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The mechanism of action of the majority of therapeutic small-molecule drugs is based on formation of a non-covalent complex with a protein binding site. In spite of the availability of thousands of crystal structures of such small-molecule ligands, important aspects of the ligand binding process are still poorly understood or at least controversially discussed. These range from fundamental biophysical aspects such as ligand conformational energies to practical aspects such as the chemical identity of the ligand 3D structure deposited in, and/or perceived from, the Protein Data Bank (PDB). A similar situation exists regarding binding data, in terms of availability as well as quality of the experimental data.
This session is therefore intended to address questions such as:
- What do we have in terms of 3D structural and binding data for ligands?
- Where are these data? How accessible, how interconnected are the databases containing them?
- To what use are these data being put? What have we learned about ligand energies?
- What are the problems, and what's still missing?
- Do we need to, and can we, annotate PDB ligands with a reliability and quality score?
Ideally, this session would lead to a consensus on some of these questions, or at least on how to approach them in a concerted effort in order to further our understanding of protein-ligand interactions.
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Presenters & Discussions Leaders
Yulia Borodina (NCBI), Reproduction of PDB Ligand structures by Conformational Ensembles at Different Energy Thresholds Abstract & Bio....
Raul Cachau (ATP, SAIC-Frederick), Chemically Accurate, Ultra-high Resolution X-ray Crystallography, Macromolecular Structure Analysis, and Drug Design Abstract & Bio....
Anne Chaka (NIST), The Need for High Quality PDB Data to Drive Improvement in Ligand Binding Predictions Abstract & Bio....
Jim Dunbar (University of Michigan), BindingMOAD - Analyzing High Quality PDB Entries with Known Binding Data Abstract & Bio....
Howard J Feldman (CCG), Using the mmCIF Dictionary for Ligand Correction Abstract & Bio....
Igor V. Filippov (NCI), A Highly Annotated SD file of all Ligand Occurrences in the PDB Abstract & Bio....
Paul Hawkins (OpenEye), Validation using the RCSB: Good Idea or Bad Idea? Abstract & Bio....
Esther Kellenberger (Univ. Strasbourg, France), PDB ligands and Drug Design: Carving out the Compound and its Cavity, and Checking out their Chemistry Abstract & Bio....
Xue Li (University of Florida), The Application of QM/MM Refinement in Protein-Ligand Complexes for Structure-Based Drug Design Abstract & Bio....
Fabrice Moriaud (MEDIT), Exploration of the Chemical Diversity Generated by the Hybridisation of PDB Ligands Abstract & Bio....
Vincent T. Moy (University of Miami), Intermolecular Forces of Cell Adhesion Molecules Abstract & Bio....
Marc Nicklaus (NCI), High Quantum-chemical Ligand Energies - True Binding Effects or Crystallographic Artifacts? Abstract & Bio....
James P. Snyder (Emory), What Energy Price Does a Drug Pay To Bind To a Protein Target? Abstract & Bio....
Chao-Yie Yang (University of Michigan), The PDBbind Database: Collection of Binding Data of the Complexes in PDB Abstract & Bio....
Janna Wehrle (NIGMS), Are we there yet? Expanding the Target-Ligand Structure & Affinity Dataset Abstract & Bio....
John Westbrook (Rutgers), Finding Small Molecules in the Protein Data Bank Archive Abstract & Bio....
Gerhard Wolber (Inte:Ligand, Austria), Structure-focused Pharmacophores for Drug Discovery from Protein-bound Ligands in the PDB Abstract & Bio....
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