Our Publications
2022
Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks
Mohammad N. Saqib, Justyna D. Kryś, Dominik Gront
Biomolecules, 2022
An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species
Malinga, N.A.; Nzuza, N.; Padayachee, T.; Syed, P.R.; Karpoormath, R.; Gront, D.; Nelson, D.R.; Syed, K.
Microorganisms, 2022
Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria.
Msweli, S.; Chonco, A.; Msweli, L.; Syed, P.R.; Karpoormath, R.; Chen, W.; Gront, D.; Nkosi, B.V.Z.; Nelson, D.R.; Syed, K.
Int. J. Mol. Sci. 2022
Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters
Nkosi, B.V.Z.; Padayachee, T.; Gront, D.; Nelson, D.R.; Syed, K.
Int. J. Mol. Sci. 2022
2021
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.
Diversification of Ferredoxins across Living Organisms
N. Nzuza, T. Padayachee, W. Chen, D. Gront, D. R. Nelson, K. Syed
O. O. Akapo , J. M. Macnar, J. D. Kryś , P. R. Syed , K. Syed, D. Gront
N. Nzuza, T. Padayachee, P. R. Syed, J. D. Kryś, W. Chen, D. Gront, D. R Nelson, K. Syed
J. D. Kryś and D. Gront
N. N. Msomi, T. Padayachee, N. Nzuza, P. R. Syed, J. D. Kryś, W. Chen, D. Gront, D. R. Nelson, K. Syed
2020
Macromolecular modeling and design in Rosetta: recent methods and frameworks
J. Koehler, B. D. Weitzner, S. M. Lewis, […], R. Bonneau
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
BioShell 3.0: Library for Processing Structural Biology Data
J. Macnar, N. Szulc, J. Kryś, A. Badaczewska-Dawid, D. Gront
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps
D. Kim, D. Gront, K. Sanbonmatsu
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
2019
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
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
2018
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly
A. Dawid, D. Gront, A. Kolinski
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
Mutation goals in the vitamin D receptor predicted by computational methods
W. Sicinska, D. Gront, K. Sicinski
2017
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
SURPASS Low-Resolution Coarse-Grained Protein Modeling
A. Dawid, D. Gront, A. Kolinski
2016
Coarse-Grained Protein Models and Their Applications
S. Kmiecik, D. Gront, M. Kolinski, L. Wieteska, A. Dawid, A. Kolinski
2015
Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima
L. Wieteska, M. Ionov, J. Szemraj, C. Feller, A. Kolinski, D. Gront
2014
BioShell-Threading: Versatile Monte Carlo package for protein 3D threading
P. Gniewek, A. Kolinski, A. Kloczkowski, D. Gront
Assessing uncertainty in the polish agricultural greenhouse gas emission inventory using monte carlo simulation
E. Wójcik-Gront, D. Gront
2013
Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics
J. Wabik, S. Kmiecik, D. Gront, M. Kouza, A. Koliński
2012
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
Optimization of profile-to-profile alignment parameters for one-dimensional threading
P. Gniewek, A. Kolinski, D. Gront
Optimization of protein models
D. Gront, S. Kmiecik, M. Blaszczyk, D. Ekonomiuk, A. Koliński
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
BioShell Threader: Protein homology detection based on sequence profiles and secondary structure profiles
D. Gront, M. Blaszczyk, P. Wojciechowski, A. Kolinski
2011
Generalized fragment picking in rosetta: Design, protocols and applications
D. Gront, D. Kulp, R. Vernon, C. Strauss, D. Baker
2009
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
2008
Fast and accurate methods for predicting short-range constraints in protein models
D. Gront, A. Kolinski
Utility library for structural bioinformatics
D. Gront, A. Kolinski
2007
Efficient scheme for optimization of parallel tempering Monte Carlo method
D. Gront, A. Kolinski
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
S. Kmiecik, D. Gront, A. Kolinski
T-Pile–a package for thermodynamic calculations for biomolecules.
D. Gront, A. Kolinski
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
D. Gront, S. Kmiecik, A. Kolinski
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
Thermodynamic properties of polypeptide chains. Parallel tempering Monte Carlo simulations
A. Sikorski, D. Gront
Comparative modeling without implicit sequence alignments
A. Kolinski, D. Gront
2006
Denatured proteins and early folding intermediates simulated in a reduced conformational space
S. Kmiecik, M. Kurcinski, A. Rutkowska, D. Gront, A. Kolinski
BioShell – a package of tools for structural biology computations
D. Gront, A. Kolinski
Clustering as a supporting tool for structural drug design.
D. Gront, M. Kurcinski, A. Kolinski
2005
A new approach to prediction of short-range conformational propensities in proteins.
D. Gront, A. Kolinski
Protein structure prediction by tempering spatial constraints
D. Gront, A. Kolinski, U. Hansmann
HCPM – Program for hierarchical clustering of protein models
D. Gront, A. Kolinski
Exploring protein energy landscapes with hierarchical clustering
D. Gront, U. Hansmann, A. Kolinski
2003
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition
A. Kolinski, D. Gront, P. Pokarowski, J. Skolnick
2001
A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics
D. Gront, A. Kolinski, J. Skolnick
2000
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
Proceedings, book chapters and other
Conference materials, book chapters and other forms of results popularisation.
2018
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
2014
Implementation and evaluation of new protocol for comparative modeling of protein structures
M. Strumillo, A. Dawid, A. Szczasiuk, D. Gront
Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS model
M. Kouza, M. Jamroz, D. Gront, S. Kmiecik, A. Koliński
Coarse-Grained Protein Models in Structure Prediction
M. Blaszczyk, D. Gront, S. Kmiecik, K. Ziolkowska, M. Panek, A. Koliński
2012
Modeling Protein Structures and their Complexes with Sparse Experimental Data
D. Gront, M. Blaszczyk, J. Wabik, A. Koliński
2014, 18 (4), 379-384
Protein Structure Prediction Using CABS – A Consensus Approach
M. Blaszczyk, M. Jamroz, D. Gront, A. Koliński
Multiscale Approach to Thermodynamics and Dynamics of a beta-Hairpin Folding
J. Wabik, D. Gront, S. Kmiecik, A. Koliński
2008
Template-Free Predictions of Three-Dimensional Protein Structures: From First Principles to Knowledge-Based Potentials
D. Gront, D. Latek, M. Kurcinski, A. Kolinski
2006
High throughput method for protein structure prediction
D. Gront, S. Kmiecik, A. Kolinski
Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational space
A. Koliński, D. Gront, S. Kmiecik, M. Kurcinski, D. Latek
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.
