Search Results - "Czaplewski, C"

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

“…In this paper, we evaluated the ability of four coarse-grained methods to predict protein flexible regions with potential biological importance, UNRES-flex,…”
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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests by 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.

“…Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The…”
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field by Chinchio, M, Czaplewski, C, Liwo, A, Ołdziej, S, Scheraga, H. A

“…Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the…”
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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 by Liwo, A., Kaźmierkiewicz, R., Czaplewski, C., Groth, M., Ołdziej, S., Wawak, R. J., Rackovsky, S., Pincus, M. R., Scheraga, H. A.

“…Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion of the average free…”
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Molecular simulations of rhodopsin tetrameter by Witt, M, Ciarkowski, J, Czaplewski, C

“…Di/oligomerization of G-protein coupled receptors (GPCRs) is well established, however very little is known regarding the interaction details. Current paper…”
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Molecular simulation study of cooperativity in hydrophobic association by CZAPLEWSKI, CEZARY, RODZIEWICZ-MOTOWIDŁO, SYLWIA, LIWO, ADAM, RIPOLL, DANIEL R., WAWAK, RYSZARD J., SCHERAGA, HAROLD A.

“…To investigate the cooperativity of hydrophobic interactions, the potential of mean force of two- and three-molecule methane clusters in water was determined…”
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds by Czaplewski, Cezary, Ołdziej, Stanisław, Liwo, Adam, Scheraga, Harold A.

“…The presence of disulfide bonds is essential for maintaining the structure and function of many proteins. The disulfide bonds are usually formed dynamically…”
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity by Ciarkowski, J, Zieleniak, A, Rodziewicz-Motowidło, S, Rusak, Ł, Chung, N N, Czaplewski, C, Witkowska, E, Schiller, P W, Izdebski, J

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The protein folding problem: global optimization of the force fields by Scheraga, H A, Liwo, A, Oldziej, S, Czaplewski, C, Pillardy, J, Ripoll, D R, Vila, J A, Kazmierkiewicz, R, Saunders, J A, Arnautova, Y A, Jagielska, A, Chinchio, M, Nanias, M

“…The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the…”
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The investigation of the effects of counterions in protein dynamics simulations by Drabik, P., Liwo, A., Czaplewski, C., Ciarkowski, J.

“…Molecular simulations able to exactly represent solvated charged proteins are helpful in understanding protein dynamics, structure and function. In the present…”
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Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3 by Malicka, Joanna, Groth, Małgorzata, Czaplewski, Cezary, Wiczk, Wiesław, Liwo, Adam

“…The conformation of a series of cyclic enkephalin analogues of a general formula X1–cyclo[Y2–Z3–Nal4–Leu5] (Nal: β‐(2‐naphthyl)alanine), where X = Tyr, Phe, or…”
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Reaction of 4-benzylidene-2-methyl-5-oxazolone with amines, Part 2: Influence of substituents in para-position in the phenyl ring and a substituent on amine nitrogen atom on the reaction kinetics by Betłakowska, B., Banecki, B., Czaplewski, C., Łankiewicz, L., Wiczk, W.

“…An influence of a structure of the amine (benzylamine, N‐methyl‐benzylamine, N‐isopropyl‐benzylamine, N‐methyl‐butylamine, N‐ethyl‐butylamine, sec‐butylamine,…”
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Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories by Kaźmierkiewicz, R, Czaplewski, C, Lammek, B, Ciarkowski, J

“…Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal…”
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Molecular modeling of the neurophysin I/oxytocin complex by Kaźmierkiewicz, R, Czaplewski, C, Lammek, B, Ciarkowski, J

“…Neurophysins I and II (NPI and NPII) act in the neurosecretory granules as carrier proteins for the neurophyseal hormones oxytocin (OT) and vasopressin (VP),…”
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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems by Liwo, Adam, Ołdziej, Stanisław, Czaplewski, Cezary, Kozłowska, Urszula, Scheraga, Harold A

“…The multibody terms pertaining to the correlation between backbone−local and backbone−electrostatic interactions in the UNRES force field for energy-based…”
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FOREWORD by C. CZAPLEWSKI, A. GIEŁDOŃ, J. LEE, A. LIWO, M. MAKOWSKI

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FOREWORD by U. H. E. HANSMANN, ADAM LIWO, C. CZAPLEWSKI

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Synthesis, activity on NK-3 tachykinin receptor and conformational solution studies of scyliorhinin II analogs modified at position 16 by Rodziewicz-Motowidło, S., Lesner, A., Łęgowska, A., Czaplewski, C., Liwo, A., Rolka, K., Patacchini, R., Quartara, L.

“…: Two analogs of a tachykinin family peptides – scyliorhinin II (ScyII): [Aib16]ScyII and [Sar16]ScyII were synthesized by the solid‐phase method using Fmoc…”
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization by Ołdziej, Stanisław, Ła̧giewka, Justyna, Liwo, Adam, Czaplewski, Cezary, Chinchio, Maurizio, Nanias, Marian, Scheraga, Harold A

“…We report the application of the hierarchical optimization method of protein potential-energy landscapes described in the accompanying papers (Liwo, A.;…”
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Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis by Rodziewicz-Motowidło, S., Łegowska, A., Qi, X.-F., Czaplewski, C., Liwo, A., Rolka, K., Sowiński, P., Mozga, W., Olczak, J., Zabrocki, J.

“…Two analogues of Scyliorhinin I (ScyI), a tachykinin with N‐MeLeu in position 8 and a 1,5‐disubstituted tetrazole ring between positions 7 and 8, introduced in…”
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