Search Results - "Lubecka, Emilia A"

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…”
Get full text

Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles by Sikorska, Emilia, Wyrzykowski, Dariusz, Szutkowski, Kosma, Greber, Katarzyna, Lubecka, Emilia A., Zhukov, Igor

“…The thermodynamic properties of micellization for dodecylphosphocholine (DPC), sodium dodecyl sulfate (SDS), and their mixtures were studied using isothermal…”
Get full text

Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions by Ślusarz, Rafał, Lubecka, Emilia A, Czaplewski, Cezary, Liwo, Adam

“…In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the…”
Get full text

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…”
Get full text

Recent Developments in Data-Assisted Modeling of Flexible Proteins by Czaplewski, Cezary, Gong, Zhou, Lubecka, Emilia A, Xue, Kai, Tang, Chun, Liwo, Adam

“…Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded…”
Get full text

A coarse‐grained approach to NMR‐data‐assisted modeling of protein structures by Lubecka, Emilia A., Liwo, Adam

“…The ESCASA algorithm for analytical estimation of proton positions from coarse‐grained geometry developed in our recent work has been implemented in modeling…”
Get full text

Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints by Lubecka, Emilia A., Liwo, Adam

“…Contact‐assisted simulations, the contacts being predicted or determined experimentally, have become very important in the determination of the structures of…”
Get full text

ESCASA: Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance‐assisted protein structure modeling. I. Backbone and Hβ protons by Lubecka, Emilia A., Liwo, Adam

“…A method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in…”
Get full text

Early Stages of RNA-Mediated Conversion of Human Prions by Lubecka, Emilia A., Hansmann, Ulrich H. E.

“…Prion diseases are characterized by the conversion of prion proteins from a PrP C fold into a disease-causing PrP SC form that is self-replicating. A possible…”
Get full text

Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins by Sieradzan, Adam K., Sans‐Duñó, Jordi, Lubecka, Emilia A., Czaplewski, Cezary, Lipska, Agnieszka G., Leszczyński, Henryk, Ocetkiewicz, Krzysztof M., Proficz, Jerzy, Czarnul, Paweł, Krawczyk, Henryk, Liwo, Adam

“…We report major algorithmic improvements of the UNRES package for physics‐based coarse‐grained simulations of proteins. These include (i) introduction of…”
Get full text

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…”
Get more information

Local and long range potentials for heparin‐protein systems for coarse‐grained simulations by Samsonov, Sergey A., Lubecka, Emilia A., Bojarski, Krzysztof K., Ganzynkowicz, Robert, Liwo, Adam

“…Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the…”
Get full text

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…”
Get full text

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…”
Get full text

Shielding effect in protein folding by Sieradzan, Adam K., Lipska, Agnieszka G., Lubecka, Emilia A.

“…[Display omitted] •The new energy function was introduced into UNited RESidue (UNRES) force field.•A new approach to take into account a shielding effect is…”
Get full text

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

Get full text

Arginine-, d-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies by Lubecka, Emilia A., Sikorska, Emilia, Sobolewski, Dariusz, Prahl, Adam, Slaninová, Jiřina, Ciarkowski, Jerzy

“…We describe the synthesis, pharmacological properties, and structures of antidiuretic agonists, arginine vasopressin (AVP) and [ d -Arg 8 ]-vasopressin (DAVP),…”
Get full text

Potent antidiuretic agonists, deamino-vasopressin and desmopressin, and their inverso analogs: NMR structure and interactions with micellar and liposomic models of cell membrane by Lubecka, Emilia A., Sikorska, Emilia, Sobolewski, Dariusz, Prahl, Adam, Slaninová, Jiřina, Ciarkowski, Jerzy

“…ABSTRACT Deamination of vasopressin (AVP) enhances its antidiuretic activity. Moreover, introduction of D‐Arg8 instead of its L enantiomer in…”
Get full text

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…”
Get full text

Conformational studies of neurohypophyseal hormones analogues with glycoconjugates by NMR spectroscopy by Lubecka, Emilia A., Sikorska, Emilia, Marcinkowska, Alina, Ciarkowski, Jerzy

“…Two glycosylated peptides have been studied using NMR spectroscopy supported by molecular modeling. Peptide I is an oxytocin (OT) analogue in which glutamine 4…”
Get full text