Search Results - "Krupa, Paweł"

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions by Liwo, Adam, Baranowski, Maciej, Czaplewski, Cezary, Gołaś, Ewa, He, Yi, Jagieła, Dawid, Krupa, Paweł, Maciejczyk, Maciej, Makowski, Mariusz, Mozolewska, Magdalena A., Niadzvedtski, Andrei, Ołdziej, Stanisław, Scheraga, Harold A., Sieradzan, Adam K., Ślusarz, Rafał, Wirecki, Tomasz, Yin, Yanping, Zaborowski, Bartłomiej

“…A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on…”
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets by He, Yi, Mozolewska, Magdalena A., Krupa, Paweł, Sieradzan, Adam K., Wirecki, Tomasz K., Liwo, Adam, Kachlishvili, Khatuna, Rackovsky, Shalom, Jagieła, Dawid, Ślusarz, Rafał, Czaplewski, Cezary R., Ołdziej, Stanisław, Scheraga, Harold A.

“…The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our…”
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11 by Krupa, Paweł, Mozolewska, Magdalena A, Wiśniewska, Marta, Yin, Yanping, He, Yi, Sieradzan, Adam K, Ganzynkowicz, Robert, Lipska, Agnieszka G, Karczyńska, Agnieszka, Ślusarz, Magdalena, Ślusarz, Rafał, Giełdoń, Artur, Czaplewski, Cezary, Jagieła, Dawid, Zaborowski, Bartłomiej, Scheraga, Harold A, Liwo, Adam

“…Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the…”
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment by Lubecka, Emilia A., Karczyńska, Agnieszka S., Lipska, Agnieszka G., Sieradzan, Adam K., Ziȩba, Karolina, Sikorska, Celina, Uciechowska, Urszula, Samsonov, Sergey A., Krupa, Paweł, Mozolewska, Magdalena A., Golon, Łukasz, Giełdoń, Artur, Czaplewski, Cezary, Ślusarz, Rafał, Ślusarz, Magdalena, Crivelli, Silvia N., Liwo, Adam

“…The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been…”
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment by Antoniak, Anna, Biskupek, Iga, Bojarski, Krzysztof K., Czaplewski, Cezary, Giełdoń, Artur, Kogut, Mateusz, Kogut, Małgorzata M., Krupa, Paweł, Lipska, Agnieszka G., Liwo, Adam, Lubecka, Emilia A., Marcisz, Mateusz, Maszota-Zieleniak, Martyna, Samsonov, Sergey A., Sieradzan, Adam K., Ślusarz, Magdalena J., Ślusarz, Rafał, Wesołowski, Patryk A., Ziȩba, Karolina

“…The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure…”
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13 by Karczyńska, Agnieszka S, Ziȩba, Karolina, Uciechowska, Urszula, Mozolewska, Magdalena A, Krupa, Paweł, Lubecka, Emilia A, Lipska, Agnieszka G, Sikorska, Celina, Samsonov, Sergey A, Sieradzan, Adam K, Giełdoń, Artur, Liwo, Adam, Ślusarz, Rafał, Ślusarz, Magdalena, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary

“…The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been…”
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Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment by Smardz, Pamela, Sieradzan, Adam K., Krupa, Paweł

“…Disulfide bonds are covalent bonds that connect nonlocal fragments of proteins, and they are unique post-translational modifications of proteins. They require…”
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations by Krupa, Paweł, Karczyńska, Agnieszka S, Mozolewska, Magdalena A, Liwo, Adam, Czaplewski, Cezary

“…Abstract Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict…”
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Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role by Krupa, Pawel, La Penna, Giovanni, Li, Mai Suan

“…Charge polarization at the membrane interface is a fundamental process in biology. Despite the lower concentration compared to the abundant monovalent ions,…”
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Exploring Structural Insights of Aβ42 and α‑Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations by Varenyk, Yuliia, Theodorakis, Panagiotis E., Pham, Dinh Q. H., Li, Mai Suan, Krupa, Paweł

“…Protein misfolding, aggregation, and fibril formation play a central role in the development of severe neurological disorders, including Alzheimer’s and…”
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Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics by Krupa, Paweł, Hałabis, Anna, Żmudzińska, Wioletta, Ołdziej, Stanisław, Scheraga, Harold A, Liwo, Adam

“…By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the…”
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Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation? by Karska, Natalia, Zhukov, Igor, Lipińska, Andrea D., Rodziewicz-Motowidło, Sylwia, Krupa, Paweł

“…Herpes simplex virus 1 (HSV-1) is a well-studied herpesvirus that causes various human diseases. Like other herpesviruses, HSV-1 produces the transmembrane…”
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Gait pattern in patients with peripheral artery disease by Szymczak, Maria, Krupa, Paweł, Oszkinis, Grzegorz, Majchrzycki, Marian

“…The aim of the present paper is to assess the gait pattern of patients with Peripheral Artery Disease (PAD). A more specific aim is to compare the gait pattern…”
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Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose by Ahmed, Lucky, Rasulev, Bakhtiyor, Kar, Supratik, Krupa, Paweł, Mozolewska, Magdalena A, Leszczynski, Jerzy

“…Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including…”
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Prediction of CD28-CD86 protein complex structure using different level of resolution approach by Krupa, Paweł, Spodzieja, Marta, Sieradzan, Adam K.

“…Immune system plays essential role in functioning of higher organisms. Its hyperactivity can lead to autoimmune diseases or even anaphylactic shock while…”
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What Makes Telomeres Unique? by Sieradzan, Adam K, Krupa, Paweł, Wales, David J

“…Telomeres are repetitive nucleotide sequences, which are essential for protecting the termini of chromosomes. Thousands of such repetitions are necessary to…”
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations by Sieradzan, Adam K, Krupa, Paweł, Scheraga, Harold A, Liwo, Adam, Czaplewski, Cezary

“…The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely,…”
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Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information by Karczyńska, Agnieszka S., Mozolewska, Magdalena A., Krupa, Paweł, Giełdoń, Artur, Liwo, Adam, Czaplewski, Cezary

“…A new approach to assisted protein–structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics…”
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A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta by Smardz, Pamela, Anila, Midhun Mohan, Rogowski, Paweł, Li, Mai Suan, Różycki, Bartosz, Krupa, Pawel

“…Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and…”
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Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies by Rogoża, Natalia H, Krupa, Magdalena A, Krupa, Pawel, Sieradzan, Adam K

“…Fullerenes, particularly C , exhibit unique properties that make them promising candidates for various applications, including drug delivery and nanomedicine…”
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