Andrzej Kolinski

39 papers Journal 37Unranked 2

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