Andrzej Kolinski

According to our database, Andrzej Kolinski authored at least 37 papers between 1993 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Integrative modeling of diverse protein-peptide systems using CABS-dock.

Wojciech Pulawski, Andrzej Kolinski, Michal Kolinski

PLoS Comput. Biol., 2023

2019

CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.

Mateusz Kurcinski, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Aleksander Kuriata, Andrzej Kolinski, Sebastian Kmiecik

Bioinform., 2019

CABS-dock standalone: a toolbox for flexible protein-peptide docking.

Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik

Bioinform., 2019

Protein-peptide docking using CABS-dock and contact information.

Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik

Briefings Bioinform., 2019

2018

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik

Nucleic Acids Res., 2018

2016

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.

Wojciech Pulawski, Michal Jamróz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik

J. Chem. Inf. Model., 2016

Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach.

Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram, Andrzej Kolinski

BMC Bioinform., 2016

Ensemble-based evaluation for protein structure models.

Michal Jamróz, Andrzej Kolinski, Daisuke Kihara

Bioinform., 2016

2015

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

Mateusz Kurcinski, Michal Jamróz, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik

Nucleic Acids Res., 2015

2014

BioShell-Threading: versatile Monte Carlo package for protein 3D threading.

Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront

BMC Bioinform., 2014

CABS-flex predictions of protein flexibility compared with NMR ensembles.

Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik

Bioinform., 2014

Flexible docking of the fragment of the troponin I to the troponin C.

Jacek Wabik, Mateusz Kurcinski, Andrzej Kolinski

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2013

CABS-flex: server for fast simulation of protein structure fluctuations.

Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik

Nucleic Acids Res., 2013

CABS-fold: server for the <i>de novo</i> and consensus-based prediction of protein structure.

Maciej Blaszczyk, Michal Jamróz, Sebastian Kmiecik, Andrzej Kolinski

Nucleic Acids Res., 2013

ClusCo: clustering and comparison of protein models.

Michal Jamróz, Andrzej Kolinski

BMC Bioinform., 2013

2012

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.

Dominik Gront, Maciej Blaszczyk, Piotr Wojciechowski, Andrzej Kolinski

Nucleic Acids Res., 2012

Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading.

Pawel Gniewek, Andrzej Kolinski, Dominik Gront

J. Comput. Biol., 2012

2011

CABS-NMR - De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.

Dorota Latek, Andrzej Kolinski

J. Comput. Chem., 2011

2010

Protein Secondary Structure Prediction using Knowledge-based Potentials.

Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski

Proceedings of the ICFC-ICNC 2010, 2010

2008

AAindex: amino acid index database, progress report 2008.

Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa

Nucleic Acids Res., 2008

Fast and accurate methods for predicting short-range constraints in protein models.

Dominik Gront, Andrzej Kolinski

J. Comput. Aided Mol. Des., 2008

Utility library for structural bioinformatics.

Dominik Gront, Andrzej Kolinski

Bioinform., 2008

2007

Protein structure prediction: Combining de novo modeling with sparse experimental data.

Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski

J. Comput. Chem., 2007

Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski

J. Comput. Chem., 2007

Comparative modeling without implicit sequence alignments.

Andrzej Kolinski, Dominik Gront

Bioinform., 2007

T-Pile - a package for thermodynamic calculations for biomolecules.

Dominik Gront, Andrzej Kolinski

Bioinform., 2007

2006

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.

Marcin Hoffmann, Krystian Eitner, Marcin von Grotthuss, Leszek Rychlewski, Ewa Banachowicz, Tomasz Grabarkiewicz, Tomasz Szkoda, Andrzej Kolinski

J. Comput. Aided Mol. Des., 2006

BioShell - a package of tools for structural biology computations.

Dominik Gront, Andrzej Kolinski

Bioinform., 2006

2005

Protein structure prediction by tempering spatial constraints.

Dominik Gront, Andrzej Kolinski, Ulrich H. E. Hansmann

J. Comput. Aided Mol. Des., 2005

HCPM - program for hierarchical clustering of protein models.

Dominik Gront, Andrzej Kolinski

Bioinform., 2005

A new approach to prediction of short-range conformational propensities in proteins.

Dominik Gront, Andrzej Kolinski

Bioinform., 2005

2003

Protein fragment reconstruction using various modeling techniques.

Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski

J. Comput. Aided Mol. Des., 2003

2001

Computational studies of protein folding.

Jeffrey Skolnick, Andrzej Kolinski

Comput. Sci. Eng., 2001

1998

Assessing energy functions for flexible docking.

Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III

J. Comput. Chem., 1998

1997

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates.

Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick

J. Comput. Chem., 1997

1993

Lattice representations of globular proteins: How good are they?

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick

J. Comput. Chem., 1993

De novo and inverse folding predictions of protein structure and dynamics.

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick

J. Comput. Aided Mol. Des., 1993