474 citations · 1.3k across the 10 of their papers we have counts for
10 papers
CABS-flex standalone 3: an open command-line platform for protein flexibility simulation, peptide structure modeling, and protein-peptide docking
Chandran Nithin, Karol Wroblewski, Piotr Szukalo +5
Summary: CABS-flex standalone 3 is an open command-line platform for fast CABS-based coarse-grained modeling of protein flexibility, peptide structures, and global or information-g…
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-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
Mateusz Kurcinski, Michal Jamroz, Maciej Blaszczyk +2
Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock we…
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…
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…