Andrzej Kolinski

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 8

Top Topics

Simulation Environment

Tandem Mass Spectra

Physicochemical Properties

Top Venues

Nucleic Acids Res.

Publications

Wojciech Pulawski, Andrzej Kolinski, Michal Kolinski
Integrative modeling of diverse protein-peptide systems using CABS-dock. PLoS Comput. Biol. 19 (7) (2023)
Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik
Protein-peptide docking using CABS-dock and contact information. Briefings Bioinform. 20 (6) (2019)
Mateusz Kurcinski, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Aleksander Kuriata, Andrzej Kolinski, Sebastian Kmiecik
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility. Bioinform. 35 (4) (2019)
Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
CABS-dock standalone: a toolbox for flexible protein-peptide docking. Bioinform. 35 (20) (2019)
Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Wojciech Pulawski, Michal Jamróz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model. J. Chem. Inf. Model. 56 (11) (2016)
Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram, Andrzej Kolinski
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. BMC Bioinform. 17 (2016)
Michal Jamróz, Andrzej Kolinski, Daisuke Kihara
Ensemble-based evaluation for protein structure models. Bioinform. 32 (12) (2016)
Mateusz Kurcinski, Michal Jamróz, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Jacek Wabik, Mateusz Kurcinski, Andrzej Kolinski
Flexible docking of the fragment of the troponin I to the troponin C. IWBBIO (2014)
Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront
BioShell-Threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinform. 15 (2014)
Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik
CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinform. 30 (15) (2014)
Michal Jamróz, Andrzej Kolinski
ClusCo: clustering and comparison of protein models CoRR (2013)
Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik
CABS-flex: server for fast simulation of protein structure fluctuations. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Michal Jamróz, Andrzej Kolinski
ClusCo: clustering and comparison of protein models. BMC Bioinform. 14 (2013)
Maciej Blaszczyk, Michal Jamróz, Sebastian Kmiecik, Andrzej Kolinski
and consensus-based prediction of protein structure. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Dominik Gront, Maciej Blaszczyk, Piotr J. Wojciechowski, Andrzej Kolinski
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Pawel Gniewek, Andrzej Kolinski, Dominik Gront
Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading. J. Comput. Biol. 19 (7) (2012)
Dorota Latek, Andrzej Kolinski
CABS-NMR - De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes. J. Comput. Chem. 32 (3) (2011)
Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski
Protein Secondary Structure Prediction using Knowledge-based Potentials. IJCCI (ICFC-ICNC) (2010)
Dominik Gront, Andrzej Kolinski
Utility library for structural bioinformatics. Bioinform. 24 (4) (2008)
Dominik Gront, Andrzej Kolinski
Fast and accurate methods for predicting short-range constraints in protein models. J. Comput. Aided Mol. Des. 22 (11) (2008)
Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36 (Database-Issue) (2008)
Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chem. 28 (9) (2007)
Andrzej Kolinski, Dominik Gront
Comparative modeling without implicit sequence alignments. Bioinform. 23 (19) (2007)
Dominik Gront, Andrzej Kolinski
T-Pile - a package for thermodynamic calculations for biomolecules. Bioinform. 23 (14) (2007)
Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski
Protein structure prediction: Combining de novo modeling with sparse experimental data. J. Comput. Chem. 28 (10) (2007)
Marcin Hoffmann, Krystian Eitner, Marcin von Grotthuss, Leszek Rychlewski, Ewa Banachowicz, Tomasz Grabarkiewicz, Tomasz Szkoda, Andrzej Kolinski
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. J. Comput. Aided Mol. Des. 20 (5) (2006)
Dominik Gront, Andrzej Kolinski
BioShell - a package of tools for structural biology computations. Bioinform. 22 (5) (2006)
Dominik Gront, Andrzej Kolinski
A new approach to prediction of short-range conformational propensities in proteins. Bioinform. 21 (7) (2005)
Dominik Gront, Andrzej Kolinski, Ulrich H. E. Hansmann
Protein structure prediction by tempering spatial constraints. J. Comput. Aided Mol. Des. 19 (8) (2005)
Dominik Gront, Andrzej Kolinski
HCPM - program for hierarchical clustering of protein models. Bioinform. 21 (14) (2005)
Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski
Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des. 17 (11) (2003)
Jeffrey Skolnick, Andrzej Kolinski
Computational studies of protein folding. Comput. Sci. Eng. 3 (5) (2001)
Jeffrey Skolnick, Andrzej Kolinski
Computational studies of protein folding. Comput. Sci. Eng. 3 (3) (2001)
Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III
Assessing energy functions for flexible docking. J. Comput. Chem. 19 (14) (1998)
Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. J. Comput. Chem. 18 (1) (1997)
Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
Lattice representations of globular proteins: How good are they? J. Comput. Chem. 14 (10) (1993)
Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. 7 (4) (1993)