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Tomasz Krzysztof Wirecki
Tomasz Krzysztof Wirecki
Postdoctoral Researcher, Institute of Molecular and Cell Biology in Warsaw
Подтвержден адрес электронной почты в домене iimcb.gov.pl - Главная страница
Название
Процитировано
Процитировано
Год
MODOMICS: a database of RNA modification pathways. 2017 update
P Boccaletto, MA Machnicka, E Purta, P Piątkowski, B Bagiński, ...
Nucleic acids research 46 (D1), D303-D307, 2018
18292018
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
I Manfredonia, C Nithin, A Ponce-Salvatierra, P Ghosh, TK Wirecki, ...
Nucleic Acids Research, 2020
2612020
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
A Liwo, M Baranowski, C Czaplewski, E Gołaś, Y He, D Jagieła, P Krupa, ...
Journal of molecular modeling 20, 1-15, 2014
1612014
WeFold: a coopetition for protein structure prediction
GA Khoury, A Liwo, F Khatib, H Zhou, G Chopra, J Bacardit, LO Bortot, ...
Proteins: Structure, Function, and Bioinformatics 82 (9), 1850-1868, 2014
772014
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Y He, MA Mozolewska, P Krupa, AK Sieradzan, TK Wirecki, A Liwo, ...
Proceedings of the National Academy of Sciences 110 (37), 14936-14941, 2013
762013
A maximum-likelihood approach to force-field calibration
B Zaborowski, D Jagieła, C Czaplewski, A Hałabis, A Lewandowska, ...
Journal of chemical information and modeling 55 (9), 2050-2070, 2015
372015
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information
P Boccaletto, M Magnus, C Almeida, A Żyła, A Astha, R Pluta, B Bagiński, ...
Nucleic acids research 46 (D1), D202-D205, 2018
332018
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
C Keasar, LJ McGuffin, B Wallner, G Chopra, B Adhikari, D Bhattacharya, ...
Scientific reports 8 (1), 9939, 2018
242018
Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
AK Sieradzan, C Czaplewski, P Krupa, MA Mozolewska, AS Karczyńska, ...
Protein folding: Methods and protocols, 399-416, 2022
212022
RNAProbe: a web server for normalization and analysis of RNA structure probing data
TK Wirecki, K Merdas, A Bernat, MJ Boniecki, JM Bujnicki, F Stefaniak
Nucleic Acids Research 48 (W1), W292-W299, 2020
202020
Modeling of Three-Dimensional RNA Structures Using SimRNA
TK Wirecki, C Nithin, S Mukherjee, JM Bujnicki, MJ Boniecki
Protein Structure Prediction, 103-125, 2020
202020
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models
J Gumna, M Antczak, RW Adamiak, JM Bujnicki, SJ Chen, F Ding, ...
International Journal of Molecular Sciences 23 (17), 9630, 2022
18*2022
SimRNAweb v2. 0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories
SN Moafinejad, BRH de Aquino, MJ Boniecki, ...
Nucleic Acids Research, gkae356, 2024
72024
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints
EF Baulin, S Mukherjee, SN Moafinejad, TK Wirecki, NG Badepally, ...
Proteins: Structure, Function, and Bioinformatics 91 (12), 1800-1810, 2023
72023
Computational Modeling Methods for 3D Structure Prediction of Ribozymes
P Ghosh, C Nithin, A Joshi, F Stefaniak, TK Wirecki, JM Bujnicki
Ribozymes 2, 861-881, 2021
32021
Microscopic Physics-Based Models of Proteins and Nucleic Acids: UNRES and NARES
M Baranowski, C Czaplewski, EI Gołaś, Y He, D Jagieła, P Krupa, A Liwo, ...
Coarse-Grained Modeling of Biomolecules, 67-120, 2017
12017
Correction to ‘SimRNAweb v2. 0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories’
MM Nikolaev, MA Farsani, NG Badepally, TK Wirecki, F Stefaniak, ...
Nucleic Acids Research, 1, 2024
2024
DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach
T Wirecki, G Lach, F Jaryani, NG Badepally, SN Moafinejad, G Klaudel, ...
bioRxiv, 2023.06. 04.543636, 2023
2023
Riboswitch-ligand structure determination using an integrative structural biology approach
A Ponce-Salvatierra, R Pluta, E Skowronek, M Orlowska, B Baginski, ...
FEBS OPEN BIO 9, 243-243, 2019
2019
Molecular Dynamics and Monte Carlo methods and their extensions for coarse-grained simulations of polypeptide folding
T Wirecki
Laboratory of Simulation of Polymers, 2016
2016
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Статьи 1–20