Sebastian Kmiecik: search on Z-Library

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1

Protein–peptide docking: opportunities and challenges

Ciemny, Maciej, Kurcinski, Mateusz, Kamel, Karol, Kolinski, Andrzej, Alam, Nawsad, Schueler-Furman, Ora, Kmiecik, Sebastian

Journal:

Drug Discovery Today

Year:

2018

Language:

english

File:

PDF, 852 KB

english, 2018

2

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations

Kurcinski, Mateusz, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

3

Coarse-Grained Protein Models and Their Applications

Kmiecik, Sebastian, Gront, Dominik, Kolinski, Michal, Wieteska, Lukasz, Dawid, Aleksandra Elzbieta, Kolinski, Andrzej

Journal:

Chemical Reviews

Year:

2016

Language:

english

File:

PDF, 6.26 MB

english, 2016

4

Geotechnical properties of products of alternative fuel combustion and co-firing with hard coal in the context of their use as solidifying dense mixtures

Stefaniak, Sebastian, Kmiecik, Ewa, Miszczak, Ewa, Plewa, Franciszek, Twardowska, Irena

Journal:

Waste Management & Research

Year:

2018

Language:

english

File:

PDF, 398 KB

english, 2018

5

Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 138 KB

english, 2007

6

Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski

Journal:

BMC Structural Biology

Year:

2007

Language:

english

File:

PDF, 5.48 MB

english, 2007

7

Optimization of protein models

Dominik Gront, Sebastian Kmiecik, Maciej Blaszczyk, Dariusz Ekonomiuk, Andrzej Koliński

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2012

Language:

english

File:

PDF, 419 KB

english, 2012

8

From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A

Kmiecik, Sebastian, Gront, Dominik, Kouza, Maksim, Kolinski, Andrzej

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 3.52 MB

english, 2012

9

Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

Kmiecik, Sebastian, Kolinski, Andrzej

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 750 KB

english, 2008

10

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

Jamroz, Michal, Orozco, Modesto, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.50 MB

english, 2013

11

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

Kmiecik, Sebastian, Jamroz, Michal, Kolinski, Michal

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 755 KB

english, 2014

12

Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism

Kmiecik, Sebastian, Kolinski, Andrzej

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 3.81 MB

english, 2011

13

Effect of weathering transformations of coal combustion residuals on trace elements mobility in view of the environmental safety and sustainability of their disposal and use. II. Element release

Stefaniak, Sebastian, Kmiecik, Ewa, Miszczak, Ewa, Szczepańska-Plewa, Jadwiga, Twardowska, Irena

Journal:

Journal of Environmental Management

Year:

2015

Language:

english

File:

PDF, 1.22 MB

english, 2015

14

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Kurcinski, Mateusz, Jamroz, Michal, Blaszczyk, Maciej, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.57 MB

english, 2015

15

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

Wabik, Jacek, Kmiecik, Sebastian, Gront, Dominik, Kouza, Maksim, Koliński, Andrzej

Journal:

International Journal of Molecular Sciences

Year:

2013

Language:

english

File:

PDF, 516 KB

english, 2013

16

Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

Blaszczyk, Maciej, Kurcinski, Mateusz, Kouza, Maksim, Wieteska, Lukasz, Debinski, Aleksander, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Year:

2015

Language:

english

File:

PDF, 3.29 MB

english, 2015

17

5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivatives

Bielenica, Anna, Kędzierska, Ewa, Koliński, Michał, Kmiecik, Sebastian, Koliński, Andrzej, Fiorino, Ferdinando, Severino, Beatrice, Magli, Elisa, Corvino, Angela, Rossi, Ilaria, Massarelli, Paola, Koz

Journal:

European Journal of Medicinal Chemistry

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

18

Protein-Peptide Docking with High Conformational Flexibility using CABS-dock Web Tool

Kouza, Maksim, Blaszczyk, Maciej, Kurcinski, Mateusz, Wieteska, Lukasz, Debinski, Aleksander, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 43 KB

english, 2016

19

SPIE Proceedings [SPIE Optics East 2005 - Boston, MA (Sunday 23 October 2005)] Advanced Environmental, Chemical, and Biological Sensing Technologies III - Assessment of chemical quality of ground waters exemplified in Major Groundwater Basin 332

Szczepanska, Jadwiga, Vo-Dinh, Tuan, Lieberman, Robert A., Kmiecik, Ewa, Twardowska, Irena, Gauglitz, Gunter, Stefaniak, Sebastian

Year:

2005

Language:

english

File:

PDF, 1.20 MB

english, 2005

20

SPIE Proceedings [SPIE Optics East 2006 - Boston, MA (Sunday 1 October 2006)] Advanced Environmental, Chemical, and Biological Sensing Technologies IV - Assessment of groundwater chemical status based on aggregated data from a monitoring network exemplified in a river drainage basin

Kmiecik, Ewa, Vo-Dinh, Tuan, Lieberman, Robert A., Stach-Kalarus, Monika, Szczepańska, Jadwiga, Gauglitz, Günter, Twardowska, Irena, Stefaniak, Sebastian, Janta-Koszuta, Krystyna

Year:

2006

Language:

english

File:

PDF, 1.35 MB

english, 2006

21

SPIE Proceedings [SPIE Optics East - Philadelphia, PA (Monday 25 October 2004)] Advanced Environmental, Chemical, and Biological Sensing Technologies II - Evaluation of temporal and spatial trends of groundwater quality alteration in the area of mining waste disposal site

Kmiecik, Ewa, Vo-Dinh, Tuan, Gauglitz, Gunter, Stefaniak, Sebastian, Szczepanska, Jadwiga, Lieberman, Robert A., Twardowska, Irena

Year:

2004

Language:

english

File:

PDF, 408 KB

english, 2004

22

Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model

Pulawski, Wojciech, Jamroz, Michal, Kolinski, Michal, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 1.07 MB

english, 2016

23

Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

Ciemny, Maciej Pawel, Debinski, Aleksander, Paczkowska, Marta, Kolinski, Andrzej, Kurcinski, Mateusz, Kmiecik, Sebastian

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.08 MB

english, 2016

24

Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligands

Bielenica, Anna, Drzewiecka-Antonik, Aleksandra, Rejmak, Paweł, Stefańska, Joanna, Koliński, Michał, Kmiecik, Sebastian, Lesyng, Bogdan, Włodarczyk, Marta, Pietrzyk, Piotr, Struga, Marta

Journal:

Journal of Inorganic Biochemistry

Year:

2018

Language:

english

File:

PDF, 5.58 MB

english, 2018

25

Leaching behavior of fly ash from co-firing of coal with alternative off gas fuel in powerplant boilers

Stefaniak, Sebastian, Kmiecik, Ewa, Miszczak, Ewa, Szczepańska-Plewa, Jadwiga, Twardowska, Irena

Journal:

Applied Geochemistry

Year:

2018

Language:

english

File:

PDF, 6.14 MB

english, 2018

26

A protocol for CABS-dock protein–peptide docking driven by side-chain contact information

Kurcinski, Mateusz, Blaszczyk, Maciej, Ciemny, Maciej Pawel, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

BioMedical Engineering OnLine

Year:

2017

Language:

english

File:

PDF, 1.65 MB

english, 2017

27

Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motif

Ciemny, Maciej Pawel, Kurcinski, Mateusz, Blaszczyk, Maciej, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

BioMedical Engineering OnLine

Year:

2017

Language:

english

File:

PDF, 1.24 MB

english, 2017

28

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Kouza, Maksim, Co, Nguyen Truong, Li, Mai Suan, Kmiecik, Sebastian, Kolinski, Andrzej, Kloczkowski, Andrzej, Buhimschi, Irina Alexandra

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.10 MB

english, 2018

29

Design and synthesis of novel 1 H -tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studies

Szulczyk, Daniel, Dobrowolski, Michał A., Roszkowski, Piotr, Bielenica, Anna, Stefańska, Joanna, Koliński, Michał, Kmiecik, Sebastian, Jóźwiak, Michał, Wrzosek, Małgorzata, Olejarz, Wioletta, Struga,

Journal:

European Journal of Medicinal Chemistry

Year:

2018

Language:

english

File:

PDF, 747 KB

english, 2018

30

CABS-flex standalone: a simulation environment for fast modeling of protein flexibility

Kurcinski, Mateusz, Oleniecki, Tymoteusz, Ciemny, Maciej Pawel, Kuriata, Aleksander, Kolinski, Andrzej, Kmiecik, Sebastian, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 209 KB

english, 2018

31

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Kuriata, Aleksander, Gierut, Aleksandra Maria, Oleniecki, Tymoteusz, Ciemny, Maciej Paweł, Kolinski, Andrzej, Kurcinski, Mateusz, Kmiecik, Sebastian

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 1.56 MB

english, 2018

32

Protein–peptide docking using CABS-dock and contact information

Blaszczyk, Maciej, Ciemny, Maciej Pawel, Kolinski, Andrzej, Kurcinski, Mateusz, Kmiecik, Sebastian

Journal:

Briefings in Bioinformatics

Year:

2018

Language:

english

File:

PDF, 12.36 MB

english, 2018

33

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Kmiecik, Sebastian, Kouza, Maksim, Badaczewska-Dawid, Aleksandra, Kloczkowski, Andrzej, Kolinski, Andrzej

Journal:

International Journal of Molecular Sciences

Year:

2018

Language:

english

File:

PDF, 3.20 MB

english, 2018

34

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

Ciemny, Maciej, Badaczewska-Dawid, Aleksandra, Pikuzinska, Monika, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

International Journal of Molecular Sciences

Year:

2019

Language:

english

File:

PDF, 2.84 MB

english, 2019

35

Aggrescan3D standalone package for structure-based prediction of protein aggregation properties

Kuriata, Aleksander, Iglesias, Valentin, Kurcinski, Mateusz, Ventura, Salvador, Kmiecik, Sebastian, Valencia, Alfonso

Journal:

Year:

2019

Language:

english

File:

PDF, 216 KB

english, 2019

36

Folding pathway of the B1 domain of protein G explored by a multiscale modeling

Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Bioentrepreneur

Year:

2007

Language:

english

File:

PDF, 1.07 MB

english, 2007

37

Folding pathway of the B1 domain of protein G explored by a multiscale modeling

Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Bioentrepreneur

Year:

2007

File:

PDF, 1.07 MB

2007

38

Flexible docking of peptides to proteins using CABS‐dock

Kurcinski, Mateusz, Badaczewska‐Dawid, Aleksandra, Kolinski, Michal, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Protein Science

Year:

2019

Language:

english

File:

PDF, 3.07 MB

english, 2019

39

Computational reconstruction of atomistic protein structures from coarse-grained models

Badaczewska-Dawid, Aleksandra E., Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Computational and Structural Biotechnology Journal

Year:

2019

File:

PDF, 1.74 MB

2019

40

Isoxazole-containing 5’ mRNA cap analogues as inhibitors of the translation initiation process

Piecyk, Karolina, Lukaszewicz, Maciej, Kamel, Karol, Janowska, Maria, Pietrow, Paulina, Kmiecik, Sebastian, Jankowska-Anyszka, Marzena

Journal:

Bioorganic Chemistry

Year:

2020

Language:

english

File:

PDF, 4.41 MB

english, 2020

41

Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation

KoliÅski, MichaÅ, Kmiecik, Sebastian, Dec, Robert, Piejko, Marcin, Mak, PaweÅ, Dzwolak, Wojciech

Journal:

International Journal of Biological Macromolecules

Year:

2020

Language:

english

File:

PDF, 1.74 MB

english, 2020

42

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement

Badaczewska-Dawid, Aleksandra E, Kmiecik, Sebastian, KoliÅski, MichaÅ

Journal:

Briefings in Bioinformatics

Year:

2020

File:

PDF, 751 KB

2020

43

Phosphorylation of the Nâterminal domain of ribosomal Pâstalk protein uL10 governs its association with the ribosome

Filipek, Kamil, MichalecâWawiÃ³rka, Barbara, Boguszewska, Aleksandra, Kmiecik, Sebastian, TchÃ³rzewski, Marek

Journal:

Year:

2020

File:

PDF, 19.32 MB

2020