Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution von Dziadek, Ł. J., Sieradzan, A. K., Czaplewski, C., Zalewski, M., Banaś, F., Toczek, M., Nisterenko, W., Grudinin, S., Liwo, A., Giełdoń, A.

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics von Liwo, Adam

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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests von Ołdziej, S., Czaplewski, C., Liwo, A., Chinchio, M., Nanias, M., Vila, J. A., Khalili, M., Arnautova, Y. A., Jagielska, A., Makowski, M., Schafroth, H. D., Kaźmierkiewicz, R., Ripoll, D. R., Pillardy, J., Saunders, J. A., Kang, Y. K., Gibson, K. D., Scheraga, H. A.

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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field von Chinchio, M, Czaplewski, C, Liwo, A, Ołdziej, S, Scheraga, H. A

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A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal... von Liwo, A., Ołdziej, S., Pincus, M. R., Wawak, R. J., Rackovsky, S., Scheraga, H. A.

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United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials von Liwo, A., Kaźmierkiewicz, R., Czaplewski, C., Groth, M., Ołdziej, S., Wawak, R. J., Rackovsky, S., Pincus, M. R., Scheraga, H. A.

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A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score... von Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S., Ołdziej, S., Scheraga, H. A.

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Ab initio Simulations of Protein-Folding Pathways by Molecular Dynamics with the United-Residue Model of Polypeptide Chains von Liwo, Adam, Khalili, Mey, Scheraga, Harold A.

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Molecular simulation study of cooperativity in hydrophobic association von CZAPLEWSKI, CEZARY, RODZIEWICZ-MOTOWIDŁO, SYLWIA, LIWO, ADAM, RIPOLL, DANIEL R., WAWAK, RYSZARD J., SCHERAGA, HAROLD A.

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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds von Czaplewski, Cezary, Ołdziej, Stanisław, Liwo, Adam, Scheraga, Harold A.

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Resolution of the excitation–emission spectra of FMN in rigid poly(vinyl alcohol) matrices von Grajek, H., Liwo, A., Wiczk, W., Żurkowska, G.

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Docking Applied to the Study of Inhibitors of c-Met Kinase von Gavernet, Luciana, Palestro, Pablo Hernan, Bruno Blanch, Luis E.

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Molecular Dynamics with the United-Residue Model of Polypeptide Chains. II. Langevin and Berendsen-Bath Dynamics and Tests on Model α-Helical Systems von Khalili, Mey, Liwo, Adam, Jagielska, Anna, Scheraga, Harold A

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Acid–base and hydrogen-bonding equilibria in aliphatic amine and carboxylic acid systems in non-aqueous solutions von Zielińska, J., Makowski, M., Maj, K., Liwo, A., Chmurzyński, L.

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Polyproline II Conformation Is One of Many Local Conformational States and Is Not an Overall Conformation of Unfolded Peptides and Proteins von Makowska, Joanna, Rodziewicz-Motowidio, Sylwia, Baginiska, Katarzyna, Vila, Jorge A., Liwo, Adam, Chmurzyński, Lech, Scheraga, Harold A.

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Combined FTIR Matrix Isolation and Density Functional Studies of Indole-3-Pyruvic Acid Molecule. Spectroscopic Evidence of Gas-Phase Tautomerism von Margonelli, Andrea, Pieretti, Andrea, Bencivenni, Luigi, Nunziante Cesaro, Stella, Mariani, Alessandro

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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins von Liwo, Jozef A., Czaplewski, Cezary R.

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The investigation of the effects of counterions in protein dynamics simulations von Drabik, P., Liwo, A., Czaplewski, C., Ciarkowski, J.

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Molecular Dynamics with the United-Residue Model of Polypeptide Chains. I. Lagrange Equations of Motion and Tests of Numerical Stability in the Microcanonical Mode von Khalili, Mey, Liwo, Adam, Rakowski, Franciszek, Grochowski, Paweł, Scheraga, Harold A

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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field von Liwo, Adam, Czaplewski, Cezary, Pillardy, Jarosław, Scheraga, Harold A.

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