474 citations · 891 across the 12 of their papers we have counts for
12 papers
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes
Maksim Kouza, Anirban Banerji, Andrzej Kolinski +2
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical resear…
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures
Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki +4
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein str…
Flexible protein-peptide docking using CABS-dock with knowledge about the binding site
Mateusz Kurcinski, Maciej Pawel Ciemny, Maciej Blaszczyk +2
Despite considerable efforts, structural prediction of protein-peptide complexes is still a very challenging task, mainly due to two reasons: high flexibility of the peptides and t…
Towards protein-protein docking with significant structural changes using CABS-dock
Maciej Pawel Ciemny, Mateusz Kurcinski, Andrzej Kolinski +1
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signal…
Highly flexible protein-peptide docking using CABS-dock
Maciej Pawel Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak +2
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process nee…
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model
Sebastian Kmiecik, Andrzej Kolinski
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the p…
Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking
Maciej Blaszczyk, Mateusz Kurcinski, Maksim Kouza +4
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical rese…
CABS-flex predictions of protein flexibility compared with NMR ensembles
Michal Jamroz, Andrzej Kolinski, Sebastian Kmiecik
Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for p…
A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain
Maksim Kouza, Chin-Kun Hu, Mai Suan Li +1
We discuss the use of a structure based C-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that…
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Jacek Wabik, Sebastian Kmiecik, Dominik Gront +2
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has b…
ClusCo: clustering and comparison of protein models
Jamróz Michał, Koliński Andrzej
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to…
Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper
Jorge Vinals, Andrzej Kolinski, Jeffrey Skolnick
A lattice based model of a protein is used to study the dimerization equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to determine the free energy of bo…