Search Results - "Perlinska AP"

Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.

Authors: Ramesh, Nikhil Ozkan, S. Banu Panagiotou, Eleni

Source: PLoS Computational Biology. 3/4/2026, Vol. 22 Issue 3, p1-17. 17p.

Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 31 topology.

Authors: Sikora M Mozajew M Sikorska JA et al.

Source: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2026 Apr 28; Vol. 123 (17), pp. e2525920123. Date of Electronic Publication: 2026 Apr 22.

Publication Type: Journal Article

Journal Info: Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE

Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens.

Authors: Perlinska AP Nguyen ML Pilla SP et al.

Source: Frontiers in molecular biosciences [Front Mol Biosci] 2024 Jun 06; Vol. 10, pp. 1223830. Date of Electronic Publication: 2024 Jun 06 (Print Publication: 2023).

Publication Type: Journal Article

Journal Info: Publisher: Frontiers Media S.A Country of Publication: Switzerland NLM ID: 101653173 Publication Model: eCollection Cited Medium: Print ISSN: 2296-889X (Print) Linking ISSN: 2296889X NLM ISO Abbreviation: Front Mol Biosci Subsets: PubMed not MEDLINE

Universe of Lasso Proteins: Exploring the Limit of Entanglement of Proteins Predicted by AlphaFold.

Authors: Bruno da Silva F Perlinska AP Płonka J et al.

Source: Journal of molecular biology [J Mol Biol] 2025 Sep 01; Vol. 437 (17), pp. 169217. Date of Electronic Publication: 2025 May 19.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

Knotted artifacts in predicted 3D RNA structures.

Authors: Gren, Bartosz A. Antczak, Maciej Zok, Tomasz et al.

Source: PLoS Computational Biology. 6/20/2024, Vol. 20 Issue 6, p1-16. 16p.

Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding.

Authors: Perlinska AP Stasiulewicz A Nguyen ML et al.

Source: PLoS computational biology [PLoS Comput Biol] 2022 Nov 21; Vol. 18 (11), pp. e1010667. Date of Electronic Publication: 2022 Nov 21 (Print Publication: 2022).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Everything AlphaFold tells us about protein knots.

Authors: Perlinska AP Sikora M Sulkowska JI

Source: Journal of molecular biology [J Mol Biol] 2024 Oct 01; Vol. 436 (19), pp. 168715. Date of Electronic Publication: 2024 Jul 17.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.

Authors: Zayats V Perlinska AP Jarmolinska AI et al.

Source: PLoS computational biology [PLoS Comput Biol] 2021 Oct 14; Vol. 17 (10), pp. e1009502. Date of Electronic Publication: 2021 Oct 14 (Print Publication: 2021).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Folding kinetics of an entangled protein.

Authors: Salicari, Leonardo Baiesi, Marco Orlandini, Enzo et al.

Source: PLoS Computational Biology. 11/13/2023, Vol. 19 Issue 11, p1-30. 30p.

Conservation of knotted and slipknotted topology in transmembrane transporters.

Authors: Zayats V Sikora M Perlinska AP et al.

Source: Biophysical journal [Biophys J] 2023 Dec 05; Vol. 122 (23), pp. 4528-4541. Date of Electronic Publication: 2023 Nov 02.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 0370626 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1542-0086 (Electronic) Linking ISSN: 00063495 NLM ISO Abbreviation: Biophys J Subsets: MEDLINE

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.

Authors: Perlinska AP Stasiulewicz A Nawrocka EK et al.

Source: PLoS computational biology [PLoS Comput Biol] 2020 May 26; Vol. 16 (5), pp. e1007904. Date of Electronic Publication: 2020 May 26 (Print Publication: 2020).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.

Authors: Jedrzejewski M Belza B Lewandowska I et al.

Source: Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2023 Aug 09; Vol. 21, pp. 3999-4008. Date of Electronic Publication: 2023 Aug 09 (Print Publication: 2023).

Publication Type: Journal Article

Journal Info: Publisher: Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology Country of Publication: Netherlands NLM ID: 101585369 Publication Model: eCollection Cited Medium: Print ISSN: 2001-0370 (Print) Linking ISSN: 20010370 NLM ISO Abbreviation: Comput Struct Biotechnol J Subsets: PubMed not MEDLINE

Structural analysis of the ribosome assembly factor Nep1, an N1‐specific pseudouridine methyltransferase, reveals mechanistic insights.

Authors: Saha, Sayan Kanaujia, Shankar Prasad

Source: FEBS Journal. May2025, Vol. 292 Issue 9, p2338-2358. 21p.

Metareview: a survey of active matter reviews.

Authors: te Vrugt, Michael Wittkowski, Raphael

Source: European Physical Journal E -- Soft Matter. Mar2025, Vol. 48 Issue 3, p1-38. 38p.

Molecular insights into natural product compounds targeting papain protease of SARS-CoV-2 through molecular dynamics simulation.

Authors: Rajchakom, Chananya Darai, Nitchakan Boonma, Thitiya et al.

Source: Chemical Monthly / Monatshefte für Chemie. Feb2025, Vol. 156 Issue 2, p219-232. 14p.

A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals.

Authors: Jimenez-Campos, Anahi G. Maestas, Lucas I. Velappan, Nileena et al.

Source: PLoS ONE. 12/26/2024, Vol. 19 Issue 12, p1-35. 35p.

Mg²⁺-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study.

Authors: Perlinska AP Kalek M Christian T et al.

Source: ACS catalysis [ACS Catal] 2020 Aug 07; Vol. 10 (15), pp. 8058-8068. Date of Electronic Publication: 2020 Jun 22.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101562209 Publication Model: Print-Electronic Cited Medium: Print ISSN: 2155-5435 (Print) NLM ISO Abbreviation: ACS Catal Subsets: PubMed not MEDLINE

Topological links in predicted protein complex structures reveal limitations of AlphaFold.

Authors: Hou, Yingnan Xie, Tengyu He, Liuqing et al.

Source: Communications Biology. 10/31/2023, Vol. 6 Issue 1, p1-10. 10p.

3D structural analysis of aptamer and diagnostic platforms for detecting hepatocellular carcinoma.

Authors: Shin, Woo-Ri Park, Dae-Young Um, Hyun-Ju et al.

Source: Molecular & Cellular Toxicology. Jul2023, Vol. 19 Issue 3, p621-634. 14p.

On topology and knotty entanglement in protein folding.

Authors: Begun, Alexander Liubimov, Sergei Molochkov, Alexander et al.

Source: PLoS ONE. 1/13/2021, Vol. 16 Issue 1, p1-17. 17p.