Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

1. Simulations of the Folding of Proteins: A Historical Perspective
Harold A. Scheraga

2. Coarse-Grained Protein Models in Structure Prediction
Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Katarzyna Ziolkowska, Marta Panek, Andrzej Kolinski

3. Coarse-Grained Modeling of Protein Dynamics
Sebastian Kmiecik, Jacek Wabik, Michal Kolinski, Maksim Kouza, Andrzej Kolinski

4. Physics-Based Modeling of Side Chain - Side Chain Interactions in the UNRES Force Field
Mariusz Makowski

5. Modeling Nucleic Acids at the Residue-Level Resolution
Filip Leonarski, Joanna Trylska

6. Modeling of Electrostatic Effects in Macromolecules
Yury N. Vorobjev

7. Optimizations of Protein Force Fields
Yoshitake Sakae, Yuko Okamoto

8. Enhanced Sampling for Biomolecular Simulations
Workalemahu Berhanu, Ping Jiang, Ulrich H. E. Hansmann

9. Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments
Alfredo E. Cardenas

10. Mechanostability of Virus Capsids and Their Proteins in Structure-Based Models
Marek Cieplak

11. Computer Modelling of the Lipid Matrix of Biomembranes
Marta Pasenkiewicz-Gierula, Michał Markiewicz

12. Modeling of Membrane Proteins
Dorota Latek, Bartosz Trzaskowski, Szymon Niewieczerzał, Przemysław Miszta, Krzysztof Młynarczyk, Aleksander Debinski, Wojciech Puławski, Shuguang Yuan, Sławomir Filipek

13. All-Atom Monte Carlo Simulations of Protein Folding and Aggregation
Anders Irbäck, Sandipan Mohanty

14. Molecular Dynamics Studies on Amyloidogenic Proteins
Sylwia Rodziewicz-Motowidło, Emilia Sikorska, Justyna Iwaszkiewicz

15. Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis
Adrien Nicolaï, Patrice Delarue, Patrick Senet

16. Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Interactions
Bálint Mészáros, Zsuzsanna Dosztányi, Csaba Magyar, István Simon

17. Theoretical and Computational Aspects of Protein Structural Alignment
Paweł Daniluk, Bogdan Lesyng

18. Simulation of the Protein Folding Process
Roterman Irena, L. Konieczny, M. Banach, D. Marchewka, B. Kalinowska, Z. Baster, M. Tomanek, M. Piwowar

19.
13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information
Jorge A. Vila, Yelena A. Arnautova

20. When Water Plays an Active Role in Electronic Structure: Insights from First-Principles Molecular Dynamics Simulations of Biological Systems
Giovanni La Penna

21. Electronic Properties of Iron Sites and Their Active Forms in Porphyrin-Type Architectures
Mariusz Radón, Ewa Broclawik

22. Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach
Tomasz Borowski, Ewa Broclawik

Avainsanat: Engineering, Computational Intelligence, Computational Biology/Bioinformatics, Protein Science, Theoretical and Computational Chemistry, Mechanics