scholarly journals Highly Flexible Protein-Peptide Docking Using CABS-Dock

2017 ◽  
pp. 69-94 ◽  
Author(s):  
Maciej Paweł Ciemny ◽  
Mateusz Kurcinski ◽  
Konrad Jakub Kozak ◽  
Andrzej Kolinski ◽  
Sebastian Kmiecik
Keyword(s):  
Peptide Docking ◽  
Flexible Protein

scholarly journals CABS-dock standalone: a toolbox for flexible protein–peptide docking

2019 ◽  
Vol 35 (20) ◽  
pp. 4170-4172 ◽  
Author(s):  
Mateusz Kurcinski ◽  
Maciej Pawel Ciemny ◽  
Tymoteusz Oleniecki ◽  
Aleksander Kuriata ◽  
Aleksandra E Badaczewska-Dawid ◽  
...  
Keyword(s):  
Docking Simulation ◽  
Computational Time ◽  
Backbone Flexibility ◽  
Non Profit ◽  
Peptide Docking ◽  
Protein Receptor ◽  
Analysis Of Results ◽  
Peptide System ◽  
Flexible Protein ◽  
Python Package

AbstractSummaryCABS-dock standalone is a multiplatform Python package for protein–peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein–peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation—it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.Availability and implementationCABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock.

Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Map Kinase ◽  
Binding Free Energy ◽  
Quantum Mechanical ◽  
Enhanced Sampling ◽  
Relative Binding ◽  
Stringent Test ◽  
Flexible Protein ◽  
P38α Map Kinase

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field is used to retrospectively calculate the relative binding free energy of a series of 17 flexible inhibitors of p38α MAP kinase. The size and flexibility of the chosen molecules represent a stringent test of the derivation of force field parameters from quantum mechanics, and enhanced sampling is required to reduce the dependence of the results on the starting structure. Competitive accuracy with a widely-used biological force field is achieved, indicating that quantum mechanics derived force fields are approaching the accuracy required to provide guidance in prospective drug discovery campaigns.</p></div></div></div>

scholarly journals Covalent Flexible Peptide Docking in Rosetta

2021 ◽  
Author(s):  
Barr Tivon ◽  
Ronen Gabizon ◽  
Bente A Somsen ◽  
Peter J Cossar ◽  
Christian Ottmann ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Peptide Docking

Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains...

Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data

2019 ◽  
Vol 59 (5) ◽  
pp. 2218-2230 ◽  
Author(s):  
Jožica Dolenc ◽  
Wilfred F. van Gunsteren ◽  
Andrea E. Prota ◽  
Michel O. Steinmetz ◽  
John H. Missimer
Keyword(s):  
Experimental Data ◽  
Chemotherapeutic Drug ◽  
Epothilone A ◽  
Conformational Properties ◽  
Flexible Protein

Flexible protein alignment and hinge detection

2002 ◽  
Vol 48 (2) ◽  
pp. 242-256 ◽  
Author(s):  
Maxim Shatsky ◽  
Ruth Nussinov ◽  
Haim J. Wolfson
Keyword(s):  
Protein Alignment ◽  
Flexible Protein

scholarly journals Elucidation of the Molecular Basis of Cholecystokinin Peptide Docking to Its Receptor Using Site-Specific Intrinsic Photoaffinity Labeling and Molecular Modeling

Biochemistry ◽  
2009 ◽  
Vol 48 (23) ◽  
pp. 5303-5312 ◽  
Author(s):  
Maoqing Dong ◽  
Polo C.-H. Lam ◽  
Delia I. Pinon ◽  
Ruben Abagyan ◽  
Laurence J. Miller
Keyword(s):  
Molecular Modeling ◽  
Molecular Basis ◽  
Photoaffinity Labeling ◽  
Site Specific ◽  
Peptide Docking

scholarly journals Energy-Filtered Electron Microscopy Reveals that Talin is a Highly Flexible Protein Composed of a Series of Globular Domains

1997 ◽  
Vol 243 (1-2) ◽  
pp. 430-436 ◽  
Author(s):  
Jorg Winkler ◽  
Heinrich Lunsdorf ◽  
Brigitte M. Jockusch
Keyword(s):  
Electron Microscopy ◽  
Flexible Protein
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