Modeling and Understanding Complex Biomolecular Systems and Processes. Application in Nanosciences, Biotechnology and Biomedicine. Bogdan Lesyng ICM and Faculty of Physiscs, Warsaw University (http://www.icm.edu.pl/~lesyng/) and European Centre of Excellence for
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Modeling and Understanding Complex Biomolecular Systems and Processes.
Application in Nanosciences, Biotechnology and Biomedicine
ICM and Faculty of Physiscs, Warsaw University (http://www.icm.edu.pl/~lesyng/)
European Centre of Excellence for
Multiscale Biomolecular Modelling,
Bioinformatics and Applications
Trento, 16-17 December, 2004
at the protein &
nucleic acids levels
3D & electronic
Dynamics, classical and/or quantum one in the real molecular environment
1 RPDFCLEPPY 10 11 TGPCKARIIR 20 21 YFYNAKAGLC 30 31 QTFVYGGCRA 40 41 KRNNFKSAED 50 51 CMRTCGGA 58
Cell(s), structure(s) & functions
Metabolic pathways & signalling
structures & processes
In our organisms
we have ~ 103
of most of
A Protein Kinase Molecule with ATP (catalytic domain)
Information, conference on
”Inhibitors of Protein Kinases”,
and workshops on
”Molecular Recognition Processes”
June 26-30, 2005 Warsaw
Recently I participated in the Robert Welch Foundation Conference on „Chemistry of Self-Organizing Hybrid Materials”, Houston, Oct.25- 26, 2004. Selected topics below:
Objects and processes listed above require, amongst others, the knowledge
of effective iteraction potentials – refer to the following port of my talk.
Microscopic generators of the potential energy function
AVB – (quantum)
AVB/GROMOS - (quantum-classical)
SCC-DFTB - (quantum)
SCC-DFTB/GROMOS - (quantum-classical)
SCC-DFTB/CHARMM - (quantum -classical)
(Self Consistent Charge Density Functional Based Tight Binding Method,
SCC DFTB, Frauenheim et al. Phys Stat. Sol. 217, 41, 2000)
basic DFT concepts:
New generation of charges capable reproducing electrostatic properties, in particular molecular dipole moments.
J.Li, T.Zhu, C.Cramer, D.Truhlar, J. Phys. Chem. A, 102, 1821(1998)
J.A. Kalinowski, B.Lesyng, J.D. Thompson, Ch.J. Cramer, D.G. Truhlar,Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Method, J. Phys. Chem. A, 108, 2545-2549 (2004)
Coulomb Field appr.
M.Feig, W.Im, C.L.Brooks, J.Chem.Phys.,120,903-911(2004)
Ratio of the GB solvation enery to the Kirkwood solvation energy
There are non-solved problems (like hydrophobic potentials), but it looks likein the near future we will have a new generation of effective (mean-field, mesoscopic) molecular interaction potentials, which can be applied to structure prediction problems (regardless of the type of biopolymers !)or ligand – biomolecule interactions.
Prof. T. FrauenheimSCC-DFTB, University of Paderborn, Germany
Dr. M. Elstner
Prof. D. TruhlarCM3-charges, Minnesota Solvation Data Base
Dr. J. ThompsonUniversity of Minnesota, USA
Dr. C. Cramer
Prof. J.A.McCammonTitration of proteins
University of California at San Diego, USA
Studies supported in part by ”European CoE for Multiscale Biomolecular Modelling, Bioinformatics and Applications” , ICM, Warsaw University.