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35 results on '"Kolinski, Michal"'

13. Protein Structure Prediction Using Coarse-Grained Models

Author

Blaszczyk, Maciej, primary, Gront, Dominik, additional, Kmiecik, Sebastian, additional, Kurcinski, Mateusz, additional, Kolinski, Michal, additional, Ciemny, Maciej Pawel, additional, Ziolkowska, Katarzyna, additional, Panek, Marta, additional, and Kolinski, Andrzej, additional

Published
2018
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18. Protein hot spots at bio-nano interfaces

Author

Audette, Gerald F., Lombardo, Stephanie, Dudzik, Jonathan, Arruda, Thomas M., Kolinski, Michal, Filipek, Slawomir, Mukerjee, Sanjeev, Kannan, Arunachala Mada, Thavasi, Velmurugan, Ramakrishna, Seeram, Chin, Michael, Somasundaran, Ponisseril, Viswanathan, Sowmya, Keles, Resat S., and Renugopalakrishnan, Venkatesan

Published
2011
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27. Flexible docking of peptides to proteins using CABS‐dock.

Author

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

Abstract

Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS‐dock is a method for protein–peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS‐dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command‐line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large‐sized systems. In this article, we outline the current status of the CABS‐dock method, its recent developments, applications, and challenges ahead. [ABSTRACT FROM AUTHOR]

Published
2020
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33. The Mechanism of Ligand-Induced Activation or Inhibition of - and -Opioid Receptors

Author

Yuan, Shuguang, Palczewski, Krzysztof, Peng, Qian, Kolinski, Michal, Vogel, Horst, and Filipek, Slawomir

Subjects
receptors, protein models, GPCRs, molecular dynamics, signal transduction
Abstract

G-protein-coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all-atom, long-time-scale molecular dynamics simulations on the -opioid and -opioid receptors (OR and OR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand-receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent-accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand.

34. Flexible docking of peptides to proteins using CABS-dock.

Author

Kurcinski M, Badaczewska-Dawid A, Kolinski M, Kolinski A, and Kmiecik S

Subjects
Binding Sites, Models, Molecular, Molecular Docking Simulation, Peptides metabolism, Protein Binding, Protein Conformation, Proteins metabolism, Software, User-Computer Interface, Web Browser, Computational Biology methods, Peptides chemistry, Proteins chemistry
Abstract

Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein-peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead., (© 2019 The Protein Society.)

Published
2020
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35. The mechanism of ligand-induced activation or inhibition of μ- and κ-opioid receptors.

Author

Yuan S, Palczewski K, Peng Q, Kolinski M, Vogel H, and Filipek S

Subjects
Ligands, Protein Binding, Protein Conformation, Signal Transduction, Receptors, Opioid, kappa metabolism, Receptors, Opioid, mu metabolism
Abstract

G-protein-coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all-atom, long-time-scale molecular dynamics simulations on the κ-opioid and μ-opioid receptors (κOR and μOR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand-receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent-accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2015
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