Our Publications


Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

S. Lyskov, S. Lewis,  J. Adolf-Bryfogle, R. Alford, K. Barlow, Z. Ben-Aharon et al.

Natur Communications, 2021 (accepted)

Diversification of Ferredoxins across Living Organisms

N. Nzuza, T. Padayachee, W. Chen, D. Gront, D. R. Nelson, K. Syed

Curr. Issues Mol. Biol. 2021, 43(3), 1374
In silico structural modeling and analysis of interactions of Tremellomycetes cytochrome P450 monooxygenases CYP51s with substrates and azoles

O. O. Akapo , J. M. Macnar, J. D. Kryś , P. R. Syed , K. Syed, D. Gront

IJMS, 2021, 22(15), 7811
Ancient bacterial class Alphaproteobacteria cytochrome P450 monooxygenases can be found in other bacterial species

N. Nzuza, T. Padayachee, P. R. Syed, J. D. Kryś, W. Chen, D. Gront, D. R Nelson, K. Syed

IJMS 2021, 22(11), 5542
VisuaLife: Library for interactive visualization in rich web applications

J. D. Kryś and D. Gront

Bioinformatics 2021, published online
In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

N. N. Msomi, T. Padayachee, N. Nzuza, P. R. Syed, J. D. Kryś, W. Chen, D. Gront, D. R. Nelson, K. Syed

Molecules 2021, 26(6), 1538


Macromolecular modeling and design in Rosetta: recent methods and frameworks

J. Koehler, B. D. Weitzner, S. M. Lewis, […], R. Bonneau

Nature Methods 2020, 17, 665-680

Better together: Elements of successful scientific software development in a distributed collaborative community

J. Koehler Leman, B. Weitzner, P.D. Renfrew, S. Lewis, R. Moretti, A. Watkins, V. Mulligan, S. Lyskov, J. Adolf-Bryfogle, J. Labonte, J. Krys, C. Bystroff, W. Schief, D. Gront, O. Schueler-Furman, D. Baker, P. Bradley, R. Dunbrack, T. Kortemme, A. Leaver-Fay, C.M. Strauss, J. Meiler, B. Kuhlman, J. Gray, R. Bonneau

PLOS Computational Biology 2020, 16 (5), e1007507

BioShell 3.0: Library for Processing Structural Biology Data

J. Macnar, N. Szulc, J. Kryś, A. Badaczewska-Dawid, D. Gront

Biomolecules 2020, 10 (3), 461

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

D. Kim, D. Gront, K. Sanbonmatsu

Journal of Chemical Information and Modeling 2020, 60 (5), 2436-2442

More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium

F. C. Mnguni, T. Padayachee, W. Chen, D. Gront, J. Yu, D. R. Nelson and K. Syed

Int. J. Mol. Sci. 2020, 21(13), 4814


Parallel Implementation of a Sequential Markov Chain in Monte Carlo Simulations of Physical Systems with Pairwise Interactions

S. Migacz, K. Dutka, P. Gumienny, M. Marchwiany, D. Gront, W. Rudnicki

Journal of Chemical Theory and Computation 2019, 15 (5), 2797-2806

Comparison of α-Helix and β-Sheet Structure Adaptation to a Quantum Dot Geometry: Toward the Identification of an Optimal Motif for a Protein Nanoparticle Cover

K. Kopeć, M. Pȩdziwiatr, D. Gront, O. Sztatelman, J. Sławski, M. Łazicka, R. Worch, K. Zawada, K. Makarova, M. Nyk, J. Grzyb

ACS Omega 2019, 4 (8), 13086-13099


Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly

A. Dawid, D. Gront, A. Kolinski

Journal of Chemical Theory and Computation 2018, 14 (4), 2277-2287

In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51

R. Matowane, L. Wieteska, H. Bamal, I. Kgosiemang, M. Van Wyk, N. Manume, S. Abdalla, S. Mashele, D. Gront, K. Syed

Biochimica et Biophysica Acta – Proteins and Proteomics 2018, 1866 (1), 166-177

Mutation goals in the vitamin D receptor predicted by computational methods

W. Sicinska, D. Gront, K. Sicinski

Journal of Steroid Biochemistry and Molecular Biology 2018, 183 , 210-220


Biofunctionalisation of p-doped silicon with cytochrome c553 minimises charge recombination and enhances photovoltaic performance of the all-solid-state photosystem I-based biophotoelectrode

J. Olmos, P. Becquet, D. Gront, J. Sar, A. Dąbrowski, G. Gawlik, M. Teodorczyk, D. Pawlak, J. Kargul

RSC Advances 2017, 7 (75), 47854-47866

SURPASS Low-Resolution Coarse-Grained Protein Modeling

A. Dawid, D. Gront, A. Kolinski

Journal of Chemical Theory and Computation 2017, 13 (11), 5766-5779


Coarse-Grained Protein Models and Their Applications

S. Kmiecik, D. Gront, M. Kolinski, L. Wieteska, A. Dawid, A. Kolinski

Chemical Reviews 2016, 116 (14), 7898-7936


Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima

L. Wieteska, M. Ionov, J. Szemraj, C. Feller, A. Kolinski, D. Gront

Journal of Biotechnology 2015, 199 , 69-76


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

P. Gniewek, A. Kolinski, A. Kloczkowski, D. Gront

BMC Bioinformatics 2014, 15 (1), 22

Assessing uncertainty in the polish agricultural greenhouse gas emission inventory using monte carlo simulation

E. Wójcik-Gront, D. Gront

Outlook on Agriculture 2014, 43 (1), 61-65


Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics

J. Wabik, S. Kmiecik, D. Gront, M. Kouza, A. Koliński

International Journal of Molecular Sciences 2013, 14 (5), 9893-9905


Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures

D. Gront, M. Grabowski, M. Zimmerman, J. Raynor, K. Tkaczuk, W. Minor

Journal of Structural and Functional Genomics 2012, 13 (4), 213-225

Optimization of profile-to-profile alignment parameters for one-dimensional threading

P. Gniewek, A. Kolinski, D. Gront

Journal of Computational Biology 2012, 19 (7), 879-886

Optimization of protein models

D. Gront, S. Kmiecik, M. Blaszczyk, D. Ekonomiuk, A. Koliński

Wiley Interdisciplinary Reviews: Computational Molecular Science 2012, 2 (3), 479-493

From coarse-grained to atomic-level characterization of protein dynamics: Transition state for the folding of B domain of protein A

S. Kmiecik, D. Gront, M. Kouza, A. Kolinski

Journal of Physical Chemistry B 2012, 116 (23), 7026-7032

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

D. Gront, M. Blaszczyk, P. Wojciechowski, A. Kolinski

Nucleic Acids Research 2012, 40 (W1),


Generalized fragment picking in rosetta: Design, protocols and applications

D. Gront, D. Kulp, R. Vernon, C. Strauss, D. Baker

PLoS ONE 2011, 6 (8), e23294


The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

S. Wang, O. Kirillova, M. Chruszcz, D. Gront, M. Zimmerman, M. Cymborowski, I. Shumilin, T. Skarina, E. Gorodichtchenskaia, A. Savchenko, A. Edwards, W. Minor

Protein Science 2009, 18 (11), 2410-2419


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

D. Gront, A. Kolinski

Journal of Computer-Aided Molecular Design 2008, 22 (11), 783-788

Utility library for structural bioinformatics

D. Gront, A. Kolinski

Bioinformatics 2008, 24 (4), 584-585


Efficient scheme for optimization of parallel tempering Monte Carlo method

D. Gront, A. Kolinski

Journal of Physics Condensed Matter 2007, 19 (3), 036225

Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

S. Kmiecik, D. Gront, A. Kolinski

BMC Structural Biology 2007, 7 , 43

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

D. Gront, A. Kolinski

Bioinformatics 2007, 23 (14), 1840-1842

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

D. Gront, S. Kmiecik, A. Kolinski

Journal of Computational Chemistry 2007, 28 (9), 1593-1597

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily

E. Ibryashkina, M. Zakharova, V. Baskunov, E. Bogdanova, M. Nagornykh, M. Den’mukhamedov, B. Melnik, A. Kolinski, D. Gront, M. Feder, A. Solonin, J. Bujnicki

BMC Structural Biology 2007, 7 , 48

Thermodynamic properties of polypeptide chains. Parallel tempering Monte Carlo simulations

A. Sikorski, D. Gront

Acta Physica Polonica B 2007, 38 (5), 1899-1908

Comparative modeling without implicit sequence alignments

A. Kolinski, D. Gront

Bioinformatics 2007, 23 (19), 2522-2527


Denatured proteins and early folding intermediates simulated in a reduced conformational space

S. Kmiecik, M. Kurcinski, A. Rutkowska, D. Gront, A. Kolinski

Acta Biochimica Polonica 2006, 53 (1), 131-143

BioShell – a package of tools for structural biology computations

D. Gront, A. Kolinski

Bioinformatics 2006, 22 (5), 621-622

Clustering as a supporting tool for structural drug design.

D. Gront, M. Kurcinski, A. Kolinski

Acta Pol Pharm 2006, 63 (5), 436-438


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

D. Gront, A. Kolinski

Bioinformatics 2005, 21 (7), 981-987

Protein structure prediction by tempering spatial constraints

D. Gront, A. Kolinski, U. Hansmann

Journal of Computer-Aided Molecular Design 2005, 19 (8), 603-608

HCPM – Program for hierarchical clustering of protein models

D. Gront, A. Kolinski

Bioinformatics 2005, 21 (14), 3179-3180

Exploring protein energy landscapes with hierarchical clustering

D. Gront, U. Hansmann, A. Kolinski

International Journal of Quantum Chemistry 2005, 105 (6), 826-830


A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition

A. Kolinski, D. Gront, P. Pokarowski, J. Skolnick

Biopolymers 2003, 69 (3), 399-405


A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics

D. Gront, A. Kolinski, J. Skolnick

The Journal of Chemical Physics 2001, 115 (3), 1569-1574


Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures

D. Gront, A. Kolinski, J. Skolnick

The Journal of Chemical Physics 2000, 113 (12), 5065-5071

Proceedings, book chapters and other

Conference materials, book chapters and other forms of results popularisation.


Protein Structure Prediction Using Coarse-Grained Models

M. Blaszczyk, D. Gront, S. Kmiecik, M. Kurcinski, M. Kolinski, C. Maciej Pawel, K. Ziolkowska, M. Panek, K. Andrzej

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes 2018, , 27-59


Implementation and evaluation of new protocol for comparative modeling of protein structures

M. Strumillo, A. Dawid, A. Szczasiuk, D. Gront

TASK Quarterly 2014, 18 (4), 379-384

Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS model

M. Kouza, M. Jamroz, D. Gront, S. Kmiecik, A. Koliński

TASK Quarterly 2014, 18 , 373-378

Coarse-Grained Protein Models in Structure Prediction

M. Blaszczyk, D. Gront, S. Kmiecik, K. Ziolkowska, M. Panek, A. Koliński

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, 2014, , 25-53


Modeling Protein Structures and their Complexes with Sparse Experimental Data

D. Gront, M. Blaszczyk, J. Wabik, A. Koliński

From Computational Biophysics to Systems Biology (CBSB11) 2012, 8 , 49-52

2014, 18 (4), 379-384

Protein Structure Prediction Using CABS – A Consensus Approach

M. Blaszczyk, M. Jamroz, D. Gront, A. Koliński

From Computational Biophysics to Systems Biology (CBSB11) Proceedings 2012, 8 , 29-32

Multiscale Approach to Thermodynamics and Dynamics of a beta-Hairpin Folding

J. Wabik, D. Gront, S. Kmiecik, A. Koliński

From Computational Biophysics to Systems Biology (CBSB11) Proceedings 2012, 8 , 213-216


Template-Free Predictions of Three-Dimensional Protein Structures: From First Principles to Knowledge-Based Potentials

D. Gront, D. Latek, M. Kurcinski, A. Kolinski

Prediction of Protein Structures, Functions, and Interactions 2008


High throughput method for protein structure prediction

D. Gront, S. Kmiecik, A. Kolinski

NIC Series 2006, 34 , 79-82

Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational space

A. Koliński, D. Gront, S. Kmiecik, M. Kurcinski, D. Latek

NIC Workshop 2006: From Computational Biophysics to System Biology 2006, 34 , 21-28

Project has been supported by:

2018/29/B/ST6/01989 NCN research grant:

,,Novel combination of  Rosetta method with SURPASS coarse grained model into a multiscale  protocol for modelling proteins and their complexes''.

The project has been realized at Warsaw University.

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Projekt i realizacja: Media Solutions Group

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