25th Molecular Modelling Workshop 2011     MGMS Logo



Program: Monday, April 4th 2011
11:30-14:00 Registration  
14:00-14:15 Welcome remarks / Agenda review  
14:15-14:35 OP 1: Matthias Dietzen (Saarbrücken)
On the Applicability of Normal Modes in Small-Molecule Docking
14:35-14:55 OP 2: Simon Leis (München)
Efficient Inclusion of Receptor Flexibility in grid-based Docking
14:55-15:15 OP 3: Alexander Gayday (Kiev)
Computational And Experimental Studies Of New Cage Compounds - Potential Antiviral Drugs
15:15-16:15 Plenary Lecture: Markus Meuwly (Basel):
Multipolar Force Fields in Chemical and Biological Simulations
16:15-16:35 Coffee break  
16:35-16:55 OP 4: Richard Bradshaw (London)
Reliably and repeatably predicting free energies by combining MM-PBSA with LES
16:55-17:15 OP 5: Anna Katharina Dehof (Saarbrücken)
A Pipeline for the training of NMR chemical shift prediction models
17:15-17:35 OP 6: Zoran Milicevic (Zagreb)
Water ordering around small hydrophobic solutes in electric fields
17:45-18:45 Annual Meeting of the MGMS-DS  
19:00 Poster Session and Buffet  

Program: Tuesday, April 5th 2011
08:30-08:50 OP 7: Jing Huang (Basel)
Efficient Computational Methods for Transition Metal Complexes: Computational Characterization of a Hydrogen-Bonded Bidentate Catalyst
08:50-09:10 OP 8: Pavlo Dral (Erlangen)
Modeling Molecular Electronic Properties with Semiempirical UNO-CAS
09:10-09:30 OP 9: Martin Richter (Jena)
SHARC - ab initio molecular dynamics with surface hopping in the adiabatic representation including arbitrary couplings
09:30-09:50 Coffee break & Conference photo  
09:50-10:10 OP 10: Matthew Mills (Manchester)
Intramolecular Polarisable Multipolar Electrostatics from a Machine Learning Method
10:10-10:30 OP 11: Thibaut Very (Vandoeuvre-ls-Nancy)
UV-VISIBLE spectra of ruthenium complexes in interaction with DNA
10:30-10:50 OP 12: Zlatko Brkljaca (Zagreb)
Conformational study of small peptides and its relation to circular dichroism spectroscopy
10:55-11:55 Plenary Lecture: Kenneth M. Merz (Florida):
How Good Do We Have to be to Solve the Protein Folding and Protein-ligand Scoring Problems?
11:55-14:00 Lunch & Posters  
14:00-14:20 OP 13: Thilo Bauer (Erlangen)
The Method of Tunneling Currents
14:20-14:40 OP 14: Karmen Condic-Jurkic (Zagreb)
New insights in protonation states of catalytic histidines in (6-4) photolyase
14:40-15:00 OP 15: Christopher Pfleger (Düsseldorf)
Robust and efficient analysis of biomacromolecular stability using ensembles of random network topologies
15:00-15:20 Coffee break  
15:20-15:40 OP 16: Markus Mühlbacher (Erlangen)
LogP as an archetype for modern QSPR
15:40-16:00 OP 17: Fatmawati Adam (Malaysia)
Force field performance in recognition of solvent mediated polymorphism of 2,6-dihydroxybenzoic acid from toluene and chloroform solution
16:00-16:20 OP 18: Fredrick Robin Devadoss Victor Paul Raj (Konstanz)
Analysis and Visual Summarization of Molecular Dynamics
16:20-17:20 Plenary Lecture: Jürgen Brickmann (Darmstadt):
"25 Years of Modelling Workshop"
18:00 Social Event: Bierkeller (Steinbach Bräu)  

Program: Wednesday, April 6th 2011
08:30-08:50 OP 19: Vedat Durmaz (Berlin)
Multi-Mode Molecular Dynamics Simulation of the Chromatographic Elution Order of Hexabromocyclododecane Stereoisomers
08:50-09:10 OP 20: Rok Borstnar (Ljubljana)
Inhibition mechanism of Monoamine Oxidase B
09:10-09:30 OP 21: Hannes Wallnoefer (Innsbruck)
Flexibility controls Specificity of Snake Venom Metalloproteases
09:30-09:50 Coffee break  
09:50-10:10 OP 22: Maurus Schmid (Basel)
Ligand Binding Study of Carbonic Anhydrase 2
10:10-10:30 OP 23: Susanne von Grafenstein (Innsbruck)
Impact of Tetramerization on Neuraminidase Dynamics
10:30-10:50 OP 24: Virginie Martiny (Paris)
Probing small-molecule binding to sulfotransferases: an in silico protocol to predict metabolism and inhibition
10:55-11:55 Plenary Lecture: Emad Tajkhorshid (Illinois):
Dynamical View of Energy Coupling Mechanisms in Active Membrane Transporters
11:55-13:50 Lunch  
13:50-14:10 OP 25: Julian Fuchs (Innsbruck)
Side Chain Oxidation Modulates Phenylalanine Hydroxylase Activity
14:10-14:30 OP 26: Shailendra Asthana (Cagliari)
Effects of point mutation on BVDV RdRp : An In-silico study
14:30-14:50 Coffee break  
14:50-15:10 OP 27: Olujide Olubiyi (Jülich)
Effects of an amyloid-inhibiting D-peptide on the conformations of the Alzheimer®s peptide
15:10-15:30 OP 28: Piotr Setny (München)
Hydration in discrete water - mean field, cellular automata based solvent model for calculating hydration free energies
15:30-15:50 OP 29: Nadine Homeyer (Düsseldorf)
Enabling medium- to high-throughput free energy calculations with the AMBER suite
16:00 Poster & Lecture awards, Closing  


P01Ali Alizadeh
Charge Configuration and its effect on Permeation through Carbon NanotubeAbstract
P02Shailendra Asthana
Effects of point mutation on BVDV RdRp : An In-silico studyAbstract
P03Frank Beierlein
A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy CalculationsAbstract
P04Rok Borstnar
Calculations of pKa and Free Energies of ComplexesAbstract
P05Alexander Bujotzek
Designing molecular spacers for multivalent ligands by modeling and simulation methodsAbstract
P06Luca Carlino
Structure-Based Design of Histone Demethylase InhibitorsAbstract
P07Anna Katharina Dehof
The Biochemical Algorithms Library (BALL) - Rapid Application Development in Structural BioinformaticsAbstract
P08Nedjoua Drici
Insight into structural properties of NCp7 proximal zinc finger: long-range electrostatic interactions effect on molecular dynamic simulationsAbstract
P09Vedat Durmaz
Multi-Mode Molecular Dynamics Simulation of the Chromatographic Elution Order of Hexabromocyclododecane StereoisomersAbstract
P10Julian Fuchs
Shape and Dynamics of Transcription Factor Binding SitesAbstract
P11Prashant Kumar Gupta
A molecular Dynamics study of water molecules with silica surface in chromatographic systemAbstract
P12Anselm Horn
Aminopyrazole β-sheet Ligands Design and Binding to Aβ42Abstract
P13Jing Zhou
Structural and functional regulation of the Focal adhesion kinase by mechanical forceAbstract
P14Christophe Jardin
Different sequence motifs of the Herpesvirus Tip protein mediate binding specificity for STAT transcription factorsAbstract
P15Kristin Kassler
A Murine CD4 Derived Peptide Scaffold to Intervene gp120-CD4 InteractionAbstract
P16Simon Leis
Efficient Inclusion of Receptor Flexibility in grid-based DockingAbstract
P17Igor Levandovskiy
Revisiting the Diels-Alder reaction: origin of selectivity and stability of endo adductsAbstract
P18Virginie Martiny
Probing small-molecule binding to sulfotransferases: an in silico protocol to predict metabolism and inhibitionAbstract
P19Heike Meiselbach
Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinaseAbstract
P20Matthew Mills
Intramolecular Polarisable Multipolar Electrostatics from a Machine Learning MethodAbstract
P21Sabine Christel Mueller
Distributed Collaborative Molecular ModellingAbstract
P22Michaela Mller
Homology model of Abcc6 provides insight into the function of mutations causing cardiovascular phenotypeAbstract
P23Stefan Nickels
Realtime Real-Time Ray Tracing in Molecular VisualizationAbstract
P24Stefan Noha
Development of a 3D pharmacophore model for inhibitors of NF-kB activation by combining structure-derived information and bias from a set of potent inhibitorsAbstract
P25Annalisa Nuccitelli
A structure-based approach to rationally design chimeric proteins for a broad-spectrum vaccine against Group B Streptococcus infections.Abstract
P26Martin Pippel
ParaDockS - An Open Source Framework for Molecular DockingAbstract
P27Kristyna Pluhackova
Structure prediction of antimicrobial peptide Melectin in membrane mimicking environmentAbstract
P28Susruta Samanta
Interaction of Polyethylene Oxide and Polypropylene Oxide with Biological InterfacesAbstract
P29Avik Sanyal
Accurate charges for transition metals in Molecular Mechanics Abstract
P30Sarah Schaefer
3D QSAR of substrates of the human H+/amino acid transporter PAT1Abstract
P31Michael Scharfe
Discovery of novel inhibitors for mono-ADP-ribosylating toxinsAbstract
P32Sebastian Schenker
(Erlangen )
Silicon cation catalyzed (3+2)-Cycloadditions: A DFT StudyAbstract
P33Sabine Schweizer
Structural Basis of Drug Resistance of Hepatitis C Virus Serine Protease VariantsAbstract
P34Dmitriy Sharapa
Polysubstituted derivates of pentacyclo[,6.03,10.05,9]undecaneAbstract
P35Inna Slynko
Homology Modeling and Docking Studies of PRK1 KinaseAbstract
P36Andrea Strasser / Hans-Joachim Wittmann
Distinct interactions between the human adrenergic β2 receptor and Gαs - an in silico studyAbstract
P37Joachim Stump
Computational analysis of the conformational stability and receptor binding properties of glycoprotein D of herpes simplex virus-1Abstract
P38Jennifer Szczesny
The Catalytic Mechanisms of Sesquiterpene Formation in Zea Mays Prenylating EnzymesAbstract
P39Ozlem Ulucan
The Role of PIF-Pocket in Modulation of PDK1 DynamicsAbstract
P40Manisha Vekaria
Predicted surface structure and crystal growth mechanism of a natural zeoliteAbstract
P41Thibaut Very
UV-VISIBLE spectra of ruthenium complexes in interaction with DNAAbstract
P42Fredrick Robin Devadoss Victor Paul Raj
Analysis of Molecular Dynamics Simulation - For Small Polypeptides and ProteinsAbstract
P43Susanne von Grafenstein
Molecular Dynamics Simulations of Neuraminidase - Subtype N1Abstract
P44Hannes Wallnoefer
Water Molecules Control Protein Structure and Ligand Affinity to fXaAbstract
P45Marcel Youmbi Foka
Comparative Study of two Classification Algorithms for the Prediction of Drug-induced PhospholipidosisAbstract
P46Vasilina Zayats
(Nove Hrady)
Structure and functions of transient receptor potential channel TRPA1Abstract
P47Wang Zhi
P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive DatasetAbstract
P48Rasoul Nasiri
Theoretical Studies on the Thermodynamics and Kinetics of the Lysine-Arginine Cross-Links Derived from α-Oxoaldehydes: A New Mechanism for Glucosepane FormationAbstract
P49Daniele Narzi
Nanodynamics of MHC:Peptide Complexes: the key to understand function and disease association?Abstract