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ORCIDAndrzej Kolinski
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Journal Articles
- 2023
[j36]Wojciech Pulawski, Andrzej Kolinski, Michal Kolinski
:
Integrative modeling of diverse protein-peptide systems using CABS-dock. PLoS Comput. Biol. 19(7) (2023)- 2019
- [j35]Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik:
Protein-peptide docking using CABS-dock and contact information. Briefings Bioinform. 20(6): 2299-2305 (2019) - [j34]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): 694-695 (2019) - [j33]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): 4170-4172 (2019) - 2018
- [j32]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): W338-W343 (2018) - 2016
- [j31]Michal Jamróz, Andrzej Kolinski, Daisuke Kihara:
Ensemble-based evaluation for protein structure models. Bioinform. 32(12): 314-321 (2016) - [j30]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: 362 (2016) - [j29]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): 2207-2215 (2016) - 2015
- [j28]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): W419-W424 (2015) - 2014
- [j27]Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik:
CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinform. 30(15): 2150-2154 (2014) - [j26]Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront:
BioShell-Threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinform. 15: 22 (2014) - 2013
- [j25]Michal Jamróz, Andrzej Kolinski:
ClusCo: clustering and comparison of protein models. BMC Bioinform. 14: 62 (2013) - [j24]Maciej Blaszczyk, Michal Jamróz, Sebastian Kmiecik, Andrzej Kolinski:
CABS-fold: server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res. 41(Webserver-Issue): 406-411 (2013) - [j23]Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik:
CABS-flex: server for fast simulation of protein structure fluctuations. Nucleic Acids Res. 41(Webserver-Issue): 427-431 (2013) - 2012
- [j22]Pawel Gniewek, Andrzej Kolinski, Dominik Gront:
Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading. J. Comput. Biol. 19(7): 879-886 (2012) - [j21]Dominik Gront, Maciej Blaszczyk, Piotr Wojciechowski, Andrzej Kolinski:
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. Nucleic Acids Res. 40(Web-Server-Issue): 257-262 (2012) - 2011
- [j20]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): 536-544 (2011) - 2008
- [j19]Dominik Gront, Andrzej Kolinski:
Utility library for structural bioinformatics. Bioinform. 24(4): 584-585 (2008) - [j18]Dominik Gront, Andrzej Kolinski:
Fast and accurate methods for predicting short-range constraints in protein models. J. Comput. Aided Mol. Des. 22(11): 783-788 (2008) - [j17]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): 202-205 (2008) - 2007
- [j16]Dominik Gront, Andrzej Kolinski:
T-Pile - a package for thermodynamic calculations for biomolecules. Bioinform. 23(14): 1840-1842 (2007) - [j15]Andrzej Kolinski, Dominik Gront:
Comparative modeling without implicit sequence alignments. Bioinform. 23(19): 2522-2527 (2007) - [j14]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): 1593-1597 (2007) - [j13]Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski:
Protein structure prediction: Combining de novo modeling with sparse experimental data. J. Comput. Chem. 28(10): 1668-1676 (2007) - 2006
- [j12]Dominik Gront, Andrzej Kolinski:
BioShell - a package of tools for structural biology computations. Bioinform. 22(5): 621-622 (2006) - [j11]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): 305-319 (2006) - 2005
- [j10]Dominik Gront, Andrzej Kolinski:
A new approach to prediction of short-range conformational propensities in proteins. Bioinform. 21(7): 981-987 (2005) - [j9]Dominik Gront, Andrzej Kolinski:
HCPM - program for hierarchical clustering of protein models. Bioinform. 21(14): 3179-3180 (2005) - [j8]Dominik Gront, Andrzej Kolinski, Ulrich H. E. Hansmann:
Protein structure prediction by tempering spatial constraints. J. Comput. Aided Mol. Des. 19(8): 603-608 (2005) - 2003
- [j7]Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski:
Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des. 17(11): 725-738 (2003) - 2001
- [j6]Jeffrey Skolnick, Andrzej Kolinski:
Computational studies of protein folding. Comput. Sci. Eng. 3(3): 40-50 (2001) - [j5]Jeffrey Skolnick, Andrzej Kolinski:
Computational studies of protein folding. Comput. Sci. Eng. 3(5): 40-50 (2001) - 1998
- [j4]Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III:
Assessing energy functions for flexible docking. J. Comput. Chem. 19(14): 1612-1622 (1998) - 1997
- [j3]Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick:
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. J. Comput. Chem. 18(1): 80-85 (1997) - 1993
- [j2]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. 7(4): 397-438 (1993) - [j1]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
Lattice representations of globular proteins: How good are they? J. Comput. Chem. 14(10): 1194-1202 (1993)
Conference and Workshop Papers
- 2014
- [c2]Jacek Wabik, Mateusz Kurcinski, Andrzej Kolinski:
Flexible docking of the fragment of the troponin I to the troponin C. IWBBIO 2014: 1064-1073 - 2010
- [c1]Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski:
Protein Secondary Structure Prediction using Knowledge-based Potentials. IJCCI (ICFC-ICNC) 2010: 370-375
Informal and Other Publications
- 2013
- [i1]Michal Jamróz, Andrzej Kolinski:
ClusCo: clustering and comparison of protein models. CoRR abs/1302.4000 (2013)
Coauthor Index
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