Search Results - "Karczyńska, Agnieszka"

Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study by Bojarski, Krzysztof K, Karczyńska, Agnieszka S, Samsonov, Sergey A

“…Procathepsins are an inactive, immature form of cathepsins, predominantly cysteine proteases present in the extracellular matrix (ECM) and in lysosomes that…”
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13 by Fajardo, J. Eduardo, Shrestha, Rojan, Gil, Nelson, Belsom, Adam, Crivelli, Silvia N., Czaplewski, Cezary, Fidelis, Krzysztof, Grudinin, Sergei, Karasikov, Mikhail, Karczyńska, Agnieszka S., Kryshtafovych, Andriy, Leitner, Alexander, Liwo, Adam, Lubecka, Emilia A., Monastyrskyy, Bohdan, Pagès, Guillaume, Rappsilber, Juri, Sieradzan, Adam K., Sikorska, Celina, Trabjerg, Esben, Fiser, Andras

“…With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can…”
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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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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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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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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 the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field by Sieradzan, Adam K, Czaplewski, Cezary, Krupa, Paweł, Mozolewska, Magdalena A, Karczyńska, Agnieszka S, Lipska, Agnieszka G, Lubecka, Emilia A, Gołaś, Ewa, Wirecki, Tomasz, Makowski, Mariusz, Ołdziej, Stanisław, Liwo, Adam

“…The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The…”
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Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins by Karczyńska, Agnieszka S, Czaplewski, Cezary, Krupa, Paweł, Mozolewska, Magdalena A, Joo, Keehyoung, Lee, Jooyoung, Liwo, Adam

“…Molecular simulations restrained to single or multiple templates are commonly used in protein‐structure modeling. However, the restraints introduce additional…”
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A Maximum-Likelihood Approach to Force-Field Calibration by Zaborowski, Bartłomiej, Jagieła, Dawid, Czaplewski, Cezary, Hałabis, Anna, Lewandowska, Agnieszka, Żmudzińska, Wioletta, Ołdziej, Stanisław, Karczyńska, Agnieszka, Omieczynski, Christian, Wirecki, Tomasz, Liwo, Adam

“…A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the…”
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13 by Fajardo, J. Eduardo, Shrestha, Rojan, Gil, Nelson, Belsom, Adam, Crivelli, Silvia N., Czaplewski, Cezary, Fidelis, Krzysztof, Grudinin, Sergei, Karasikov, Mikhail, Karczyńska, Agnieszka S., Kryshtafovych, Andriy, Leitner, Alexander, Liwo, Adam, Lubecka, Emilia A., Monastyrskyy, Bohdan, Pagès, Guillaume, Rappsilber, Juri, Sieradzan, Adam K., Sikorska, Celina, Trabjerg, Esben, Fiser, Andras

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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics by Czaplewski, Cezary, Karczyńska, Agnieszka, Sieradzan, Adam K, Liwo, Adam

“…Abstract A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES…”
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BTLA-derived peptides as inhibitors of BTLA/HVEM complex formation – design, synthesis and biological evaluation by Kuncewicz, Katarzyna, Bojko, Magdalena, Battin, Claire, Karczyńska, Agnieszka, Sieradzan, Adam, Sikorska, Emilia, Węgrzyn, Katarzyna, Wojciechowicz, Karolina, Wardowska, Anna, Steinberger, Peter, Rodziewicz-Motowidło, Sylwia, Spodzieja, Marta

“…Immune checkpoints can be divided into co-stimulatory and co-inhibitory molecules that regulate the activation and effector functions of T cells. The…”
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Fragments of gD Protein as Inhibitors of BTLA/HVEM Complex Formation-Design, Synthesis, and Cellular Studies by Kuncewicz, Katarzyna, Battin, Claire, Sieradzan, Adam, Karczyńska, Agnieszka, Orlikowska, Marta, Wardowska, Anna, Pikuła, Michał, Steinberger, Peter, Rodziewicz-Motowidło, Sylwia, Spodzieja, Marta

“…One of the major current trends in cancer immunotherapy is the blockade of immune checkpoint proteins that negatively regulate the immune response. This has…”
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Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding by Spodzieja, Marta, Kuncewicz, Katarzyna, Sieradzan, Adam, Karczyńska, Agnieszka, Iwaszkiewicz, Justyna, Cesson, Valérie, Węgrzyn, Katarzyna, Zhukov, Igor, Maszota-Zieleniak, Martyna, Michielin, Olivier, Speiser, Daniel E, Zoete, Vincent, Derré, Laurent, Rodziewicz-Motowidło, Sylwia

“…Immune checkpoints are crucial in the maintenance of antitumor immune responses. The activation or blockade of immune checkpoints is dependent on the…”
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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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Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability by Gitlin-Domagalska, Agata, Dębowski, Dawid, Gucwa, Katarzyna, Starego, Dominika, Ptaszyńska, Natalia, Sieradzan, Adam, Karczyńska, Agnieszka, Samsonov, Sergey A., Mangold, Martin, Gütschow, Michael, Łęgowska, Anna, Rolka, Krzysztof

“…A gradual truncation of the primary structure of frog skin-derived Huia versabilis Bowman-Birk peptidic inhibitor (HV-BBI) resulted in 18-times stronger…”
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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets by Karczyńska, Agnieszka, Mozolewska, Magdalena A., Krupa, Paweł, Giełdoń, Artur, Bojarski, Krzysztof K., Zaborowski, Bartłomiej, Liwo, Adam, Ślusarz, Rafał, Ślusarz, Magdalena, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary

“…Knowledge-based methods are, at present, the most effective ones for the prediction of protein structures; however, their results heavily depend on the…”
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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers by Liwo, Adam, Czaplewski, Cezary, Sieradzan, Adam K, Lubecka, Emilia A, Lipska, Agnieszka G, Golon, Łukasz, Karczyńska, Agnieszka, Krupa, Paweł, Mozolewska, Magdalena A, Makowski, Mariusz, Ganzynkowicz, Robert, Giełdoń, Artur, Maciejczyk, Maciej

“…In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective…”
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A structural model of the immune checkpoint CD160-HVEM complex derived from HDX-mass spectrometry and molecular modeling by Kuncewicz, Katarzyna, Spodzieja, Marta, Sieradzan, Adam, Karczyńska, Agnieszka, Dąbrowska, Katarzyna, Dadlez, Michał, Speiser, Daniel E, Derre, Laurent, Rodziewicz-Motowidło, Sylwia

“…CD160 is a T cell coinhibitory molecule that interacts with the herpes virus entry mediator (HVEM) on antigen-presenting cells to provide an inhibitory signal…”
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INVESTIGATION OF INTERACTIONS BETWEEN DERMORPHIN ANALOGS AND µ-OPIOID RECEPTOR by AGNIESZKA KARCZYŃSKA, BARTŁOMIEJ ZABOROWSKI, MAGDALENA ŚLUSARZ

“…Opioid receptors play the pain control function in the body. Most of the research is carried out to find the most effective analgesic. The earliest analgesic…”
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