Search Results - "Wirecki, Tomasz"

MODOMICS: a database of RNA modification pathways. 2017 update by Boccaletto, Pietro, Machnicka, Magdalena A, Purta, Elzbieta, Piątkowski, Paweł, Bagiński, Błażej, Wirecki, Tomasz K, de Crécy-Lagard, Valérie, Ross, Robert, Limbach, Patrick A, Kotter, Annika, Helm, Mark, Bujnicki, Janusz M

“…Abstract MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides,…”
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Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements by Manfredonia, Ilaria, Nithin, Chandran, Ponce-Salvatierra, Almudena, Ghosh, Pritha, Wirecki, Tomasz K, Marinus, Tycho, Ogando, Natacha S, Snijder, Eric J, van Hemert, Martijn J, Bujnicki, Janusz M, Incarnato, Danny

“…Abstract SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The…”
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SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories by Moafinejad, S Naeim, de Aquino, Belisa R H, Boniecki, Michał J, Pandaranadar Jeyeram, Iswarya P N, Nikolaev, Grigory, Magnus, Marcin, Farsani, Masoud Amiri, Badepally, Nagendar Goud, Wirecki, Tomasz K, Stefaniak, Filip, Bujnicki, Janusz M

“…Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional…”
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RNAProbe: a web server for normalization and analysis of RNA structure probing data by Wirecki, Tomasz K, Merdas, Katarzyna, Bernat, Agata, Boniecki, Michał J, Bujnicki, Janusz M, Stefaniak, Filip

“…Abstract RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of…”
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Modeling of Three-Dimensional RNA Structures Using SimRNA by Wirecki, Tomasz K, Nithin, Chandran, Mukherjee, Sunandan, Bujnicki, Janusz M, Boniecki, Michał J

“…The molecules of the ribonucleic acid (RNA) perform a variety of vital roles in all living cells. Their biological function depends on their structure and…”
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RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints by Baulin, Eugene F., Mukherjee, Sunandan, Moafinejad, S. Naeim, Wirecki, Tomasz K., Badepally, Nagendar Goud, Jaryani, Farhang, Stefaniak, Filip, Amiri Farsani, Masoud, Ray, Angana, Rocha de Moura, Tales, Bujnicki, Janusz M.

“…Ribonucleic acid (RNA) molecules serve as master regulators of cells by encoding their biological function in the ribonucleotide sequence, particularly their…”
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets by He, Yi, Mozolewska, Magdalena A., Krupa, Paweł, Sieradzan, Adam K., Wirecki, Tomasz K., Liwo, Adam, Kachlishvili, Khatuna, Rackovsky, Shalom, Jagieła, Dawid, Ślusarz, Rafał, Czaplewski, Cezary R., Ołdziej, Stanisław, Scheraga, Harold A.

“…The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our…”
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Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models by Gumna, Julita, Antczak, Maciej, Adamiak, Ryszard W, Bujnicki, Janusz M, Chen, Shi-Jie, Ding, Feng, Ghosh, Pritha, Li, Jun, Mukherjee, Sunandan, Nithin, Chandran, Pachulska-Wieczorek, Katarzyna, Ponce-Salvatierra, Almudena, Popenda, Mariusz, Sarzynska, Joanna, Wirecki, Tomasz, Zhang, Dong, Zhang, Sicheng, Zok, Tomasz, Westhof, Eric, Miao, Zhichao, Szachniuk, Marta, Rybarczyk, Agnieszka

“…RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since…”
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RNArchitecture: a database and a classification system of RNA families, with a focus on structural information by Boccaletto, Pietro, Magnus, Marcin, Almeida, Catarina, Żyła, Adriana, Astha, Astha, Pluta, Radosław, Bagiński, Błażej, Jankowska, Elżbieta, Dunin-Horkawicz, Stanisław, Wirecki, Tomasz K, Boniecki, Michał J, Stefaniak, Filip, Bujnicki, Janusz M

“…Abstract RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a…”
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions by Liwo, Adam, Baranowski, Maciej, Czaplewski, Cezary, Gołaś, Ewa, He, Yi, Jagieła, Dawid, Krupa, Paweł, Maciejczyk, Maciej, Makowski, Mariusz, Mozolewska, Magdalena A., Niadzvedtski, Andrei, Ołdziej, Stanisław, Scheraga, Harold A., Sieradzan, Adam K., Ślusarz, Rafał, Wirecki, Tomasz, Yin, Yanping, Zaborowski, Bartłomiej

“…A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on…”
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field by Sieradzan, Adam K, Czaplewski, Cezary, Krupa, Paweł, Mozolewska, Magdalena A, Karczyńska, Agnieszka S, Lipska, Agnieszka G, Lubecka, Emilia A, Gołaś, Ewa, Wirecki, Tomasz, Makowski, Mariusz, Ołdziej, Stanisław, Liwo, Adam

“…The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The…”
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WeFold: A coopetition for protein structure prediction by Khoury, George A., Liwo, Adam, Khatib, Firas, Zhou, Hongyi, Chopra, Gaurav, Bacardit, Jaume, Bortot, Leandro O., Faccioli, Rodrigo A., Deng, Xin, He, Yi, Krupa, Pawel, Li, Jilong, Mozolewska, Magdalena A., Sieradzan, Adam K., Smadbeck, James, Wirecki, Tomasz, Cooper, Seth, Flatten, Jeff, Xu, Kefan, Baker, David, Cheng, Jianlin, Delbem, Alexandre C. B., Floudas, Christodoulos A., Keasar, Chen, Levitt, Michael, Popović, Zoran, Scheraga, Harold A., Skolnick, Jeffrey, Crivelli, Silvia N., Players, Foldit

“…ABSTRACT The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the…”
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A Maximum-Likelihood Approach to Force-Field Calibration by Zaborowski, Bartłomiej, Jagieła, Dawid, Czaplewski, Cezary, Hałabis, Anna, Lewandowska, Agnieszka, Żmudzińska, Wioletta, Ołdziej, Stanisław, Karczyńska, Agnieszka, Omieczynski, Christian, Wirecki, Tomasz, Liwo, Adam

“…A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the…”
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WeFold: A coopetition for protein structure prediction: WeFold Protein Structure Prediction Coopetition by Khoury, George A., Liwo, Adam, Khatib, Firas, Zhou, Hongyi, Chopra, Gaurav, Bacardit, Jaume, Bortot, Leandro O., Faccioli, Rodrigo A., Deng, Xin, He, Yi, Krupa, Pawel, Li, Jilong, Mozolewska, Magdalena A., Sieradzan, Adam K., Smadbeck, James, Wirecki, Tomasz, Cooper, Seth, Flatten, Jeff, Xu, Kefan, Baker, David, Cheng, Jianlin, Delbem, Alexandre C. B., Floudas, Christodoulos A., Keasar, Chen, Levitt, Michael, Popović, Zoran, Scheraga, Harold A., Skolnick, Jeffrey, Crivelli, Silvia N., Players, Foldit

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