Workshop on

Modeling Interactions in Biomolecules II

Prague, September 5th 9th, 2005

Scientific Programme
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Scientific Programme

Monday 10:00-16:00 Registration
(Chairman) 16:00-16:10 Burda Opening
16:10-16:20 Okojie Greetings from JSU
16:20-16:40 Němeček Magnetohydrodynamics (MHD) and Particle Modeling of the Solar Wind - Magnetosphere Interaction
16:40-17:10 Skála Probabilistic Approach To Understanding Quantum Mechanics
coffee break
17:30-18:20 Politzer Halogen Bonding
19:00 Reception
Clark 9:00-9:45 Kozelka Modeling Platinum-DNA Interactions
9:45-10:30 Blomberg Modeling reactions of cytochrome c oxidase
coffee break
10:50-11:20 Broclawik Reaction mechanism for the metabolism of antimigraine drugs on iron site in cytochrome P450 enzymes
11:20-11:50 Murray Computational Studies of Halogenated Hydrocarbon Anesthetics
11:50-12:20 Michalak Bond-Orders and Bond-Orbitals
Mohamed 14:00-14:30 Leszczynski Structure and Properties of DNA Fragments
14:30-15:00 Shishkin Molecular Structure, Relative stability of Conformers and Intramolecular Hydrogen Bonds in Canonical 2\\\'-Deoxyribonucleotides
15:00-15:30 Schreiber Ground and excited state properties of non-complementary metal--DNA base pairs
coffee break
15:50-16:10 Meyer Systematic quantum chemical studies of nucleic acid bases
16:10-16:30 Nachtigallová Theoretical study of excited states of 7-methyl-Guanine and 9-methyl-Guanine
16:30-16:50 Robertazzi Pi-Stacking in Aromatic Complexes. An Atoms in Molecules and DFT Study
16:50-17:10 Řeha Thermodynamic Stability of DNA Duplex Modified by Nonpolar Base Analogues
coffee break
17:30-17:50 Rutkowska-Zbik DFT Studies on Ligand Binding Properties of Cobalamins
17:50-18:10 Gossens DNA-Binding Of Ruthenium-Arene Anticancer Drugs
18:10-18:30 Dudev Metal Selectivity in Metalloproteins
18:30-18:50 Rázga RNA K-turns - A flexible ribosomal motifs
18:50-19:10 Valdes Phenylalanyl-Glycyl-Glycine Tripetide in the Gas-Phase: A step forward to understand geometry protein structures
Sokalski 9:00-9:45 Clark New methods for simulating biological systems
9:45-10:30 Lim A Novel Forcefield including Ligand?Metal Charge Transfer and Local Polarization for Zn Protein Simulations
coffee break
10:50-11:20 Cruz Conceptual DFT descriptors to model organometallic reactivity
11:20-11:50 Toro-Labbe Reaction Force. A Key Concept to Characterize Reaction Mechanisms
Blomberg 9:00-9:30 Sun Examination of Folding of Two Short Helical Peptides Using Molecular Dynamics Simulation
9:30-10:00 Wesolowski First-principles based multi-level computer simulation studies of complex materials
10:00-10:30 Šponer Molecular dynamics simulations of RNA molecules.
coffee break
10:50-11:20 Luque Ligand access in trucated hemoglobin HbN
11:20-11:50 Sugihara Modellining of the Rhodopsin Chromophore
11:50-12:20 Rulíšek QM/MM modelling of the redox active sites in metalloproteins
Kozelka 14:00-14:30 Gresh Refinements and Validation of Anisotropic Polarizable Molecular Mechanics. Applications to inhibitor-metalloenzyme complexes.
14:30-15:00 Sundholm Ab initio and density-functional studies of nanomolecules
15:00-15:30 Bondar Mechanism of the retinal deprotonation step in the bacteriorhodopsin photocycle
coffee break
15:50-16:20 Fadrná Influence of ion parameters on molecular dynamics and/or free energy calculation
16:20-16:40 Zhygalko Long-residency hydration, cation binding, and dynamics of Hepatitis Delta Virus ribozyme
16:40-17:00 Waller A New Charge Density Method Applied To The Neurotransmitter Taurine
17:00-17:20 Rungrotmongkol Modelling the enzymatic reaction of HIV-1 reverse transcriptase based on combined quantum mechanical and molecular mechanical (QM/MM) approach
coffee break
17:40-18:00 Andruniow Mechanism of the Initial Conformational Transition of a Photomodulable Peptide
18:00-18:20 Szefczyk Differential transition state stabilization in chorismate mutase
18:20-18:40 Kedzierski Visualization of molecular and catalytic properties
19:00-19:20 Chidthong Study of the Electronic and Absorption Properties of the Fluorene-Pyridine Conjugated Polymers by Theoretical Investigation
Koca 9:00-9:30 Ruud The ab initio calculation of Raman Optical Activity
9:30-10:00 Sychrovský Calculation of NMR spin-spin coupling constants in bio-molecular complexes and their correlation with the molecular structure
10:00-10:30 Bliznyuk What can be learned from semi-empirical and ab-initio calculations of large biological systems
coffee break
10:50-11:20 Mulholland Insights into enzyme mechanism and catalysis from QM/MM modelling
11:20-11:50 Renugopalakrishnan Protein-based Memory
11:50-12:00 closing remarks


Up to date information is now available:
Scientific Programme
Practical Information
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Registration is no longer possible.

The 11th International Conference on the Application of Density Functional Theory in Chemistry and Physics will be held in Geneva in September 11-15, 2005.

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