Protein–Protein and Protein–Peptide Docking with ClusPro Server

2020 ◽  
pp. 157-174
Author(s):  
Andrey Alekseenko ◽  
Mikhail Ignatov ◽  
George Jones ◽  
Maria Sabitova ◽  
Dima Kozakov
Keyword(s):  
Peptide Docking

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...

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 Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

scholarly journals dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

2016 ◽  
Vol 3 ◽  
Author(s):  
Dimitrios Spiliotopoulos ◽  
Panagiotis L. Kastritis ◽  
Adrien S. J. Melquiond ◽  
Alexandre M. J. J. Bonvin ◽  
Giovanna Musco ◽  
...  
Keyword(s):  
Scoring Function ◽  
Peptide Docking

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides

2018 ◽  
Vol 58 (6) ◽  
pp. 1292-1302 ◽  
Author(s):  
Pei Zhou ◽  
Botong Li ◽  
Yumeng Yan ◽  
Bowen Jin ◽  
Libang Wang ◽  
...  
Keyword(s):  
Conformer Generation ◽  
Ensemble Docking ◽  
Peptide Docking

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.

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

2016 ◽  
Vol 110 (3) ◽  
pp. 543a
Author(s):  
Maksim Kouza ◽  
Maciej Blaszczyk ◽  
Mateusz Kurcinski ◽  
Lukasz Wieteska ◽  
Aleksander Debinski ◽  
...  
Keyword(s):  
Conformational Flexibility ◽  
Web Tool ◽  
Peptide Docking

Peptide docking of HIV-1 p24 with single chain fragment variable (scFv) by CDOCKER algorithm

2014 ◽  
Author(s):  
Hana Atiqah Abdul Karim ◽  
Chatchai Tayapiwatana ◽  
Piyarat Nimmanpipug ◽  
Sharifuddin M. Zain ◽  
Noorsaadah Abdul Rahman ◽  
...  
Keyword(s):  
Single Chain ◽  
Chain Fragment ◽  
Peptide Docking ◽  
Single Chain Fragment Variable ◽  
Hiv 1 ◽  
Single Chain Fragment

Identification of novel MAGE-A6- and MAGE-A12-derived HLA-A24-restricted cytotoxic T lymphocyte epitopes using an in silico peptide-docking assay

2012 ◽  
Vol 61 (12) ◽  
pp. 2311-2319 ◽  
Author(s):  
Yasuto Akiyama ◽  
Masaru Komiyama ◽  
Yoji Nakamura ◽  
Akira Iizuka ◽  
Chie Oshita ◽  
...  
Keyword(s):  
T Lymphocyte ◽  
In Silico ◽  
Cytotoxic T Lymphocyte ◽  
Peptide Docking
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