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AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. W1, p. W187, doi. 10.1093/nar/gkae443
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- Article
Knot or not? Identifying unknotted proteins in knotted families with sequence‐based Machine Learning model.
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- Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 7, p. 1, doi. 10.1002/pro.4998
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- Article
Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens.
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- Frontiers in Molecular Biosciences, 2024, p. 01, doi. 10.3389/fmolb.2023.1223830
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- Article
Knotted artifacts in predicted 3D RNA structures.
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- PLoS Computational Biology, 2024, v. 20, n. 6, p. 1, doi. 10.1371/journal.pcbi.1011959
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- Article
AlphaFold predicts novel human proteins with knots.
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- Protein Science: A Publication of the Protein Society, 2023, v. 32, n. 5, p. 1, doi. 10.1002/pro.4631
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- Article
Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding.
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- PLoS Computational Biology, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.pcbi.1010667
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- Article
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods.
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- Nucleic Acids Research, 2022, v. 50, n. W1, p. W44, doi. 10.1093/nar/gkac388
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- Article
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
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- PLoS Computational Biology, 2021, v. 17, n. 10, p. 1, doi. 10.1371/journal.pcbi.1009502
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- Article
SARS-CoV-2 Papain-Like Protease Potential Inhibitors—In Silico Quantitative Assessment.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 8, p. 3957, doi. 10.3390/ijms22083957
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- Article
GLN: a method to reveal unique properties of lasso type topology in proteins.
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- Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-71874-2
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- Article
The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots.
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- Israel Journal of Chemistry, 2020, v. 60, n. 7, p. 713, doi. 10.1002/ijch.202000036
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- Article
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.
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- PLoS Computational Biology, 2020, v. 16, n. 5, p. 1, doi. 10.1371/journal.pcbi.1007904
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- Article
A Guide to Targeting the Endocannabinoid System in Drug Design.
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- International Journal of Molecular Sciences, 2020, v. 21, n. 8, p. 2778, doi. 10.3390/ijms21082778
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- Article
Knot_pull—python package for biopolymer smoothing and knot detection.
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- Bioinformatics, 2020, v. 36, n. 3, p. 953, doi. 10.1093/bioinformatics/btz644
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- Article
Genus for biomolecules.
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- Nucleic Acids Research, 2020, v. 48, n. D1, p. D1129, doi. 10.1093/nar/gkz845
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- Article
PyLink: a PyMOL plugin to identify links.
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- Bioinformatics, 2019, v. 35, n. 17, p. 3166, doi. 10.1093/bioinformatics/bty1038
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- Article
Defining and detecting links in chromosomes.
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- Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-47999-4
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- Article
Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function.
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- Polymers (20734360), 2019, v. 11, n. 4, p. 707, doi. 10.3390/polym11040707
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- Article
KnotProt 2.0: a database of proteins with knots and other entangled structures.
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- Nucleic Acids Research, 2019, v. 47, n. D1, p. D367, doi. 10.1093/nar/gky1140
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- Article
Genus trace reveals the topological complexity and domain structure of biomolecules.
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- Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-35557-3
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- Article
GapRepairer: a server to model a structural gap and validate it using topological analysis.
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- Bioinformatics, 2018, v. 34, n. 19, p. 3300, doi. 10.1093/bioinformatics/bty334
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- Article
KnotGenome: a server to analyze entanglements of chromosomes.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W17, doi. 10.1093/nar/gky511
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- Article
The exclusive effects of chaperonin on the behavior of proteins with 5<sub>2</sub> knot.
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- PLoS Computational Biology, 2018, v. 14, n. 3, p. 1, doi. 10.1371/journal.pcbi.1005970
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- Article
PyLasso: a PyMOL plugin to identify lassos.
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- Bioinformatics, 2017, v. 33, n. 23, p. 3819, doi. 10.1093/bioinformatics/btx493
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- Article
To Tie or Not to Tie? That Is the Question.
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- Polymers (20734360), 2017, v. 9, n. 9, p. 454, doi. 10.3390/polym9090454
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- Article
Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume.
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- PLoS ONE, 2017, v. 12, n. 5, p. 1, doi. 10.1371/journal.pone.0176744
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- Article
LinkProt: a database collecting information about biological links.
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- Nucleic Acids Research, 2017, v. 45, n. D1, p. D243, doi. 10.1093/nar/gkw976
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- Article
Complex lasso: new entangled motifs in proteins.
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- Scientific Reports, 2016, p. 36895, doi. 10.1038/srep36895
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- Article
In Search of Functional Advantages of Knots in Proteins.
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- PLoS ONE, 2016, v. 11, n. 11, p. 1, doi. 10.1371/journal.pone.0165986
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- Article
LassoProt: server to analyze biopolymers with lassos.
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- Nucleic Acids Research, 2016, v. 44, n. W1, p. W383, doi. 10.1093/nar/gkw308
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- Article
KnotProt: a database of proteins with knots and slipknots.
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- Nucleic Acids Research, 2015, v. 43, n. D1, p. D306, doi. 10.1093/nar/gku1059
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- Article
Pierced Lasso Bundles Are a New Class of Knot-like Motifs.
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- PLoS Computational Biology, 2014, v. 10, n. 6, p. 1, doi. 10.1371/journal.pcbi.1003613
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- Article
Knotting pathways in proteins.
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- Biochemical Society Transactions, 2013, v. 41, n. 2, p. 523, doi. 10.1042/BST20120342
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- Article
Identifying knots in proteins.
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- Biochemical Society Transactions, 2013, v. 41, n. 2, p. 533, doi. 10.1042/BST20120339
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- Article
Knot localization in proteins.
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- Biochemical Society Transactions, 2013, v. 41, n. 2, p. 538, doi. 10.1042/BST20120329
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- Article
The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin.
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- PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045654
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- Article
BSDB: the biomolecule stretching database.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D443, doi. 10.1093/nar/gkq851
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- Article
A Stevedore's Protein Knot.
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- PLoS Computational Biology, 2010, v. 6, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000731
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- Article
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots.
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- PLoS Computational Biology, 2009, v. 5, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000547
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- Article
Predicting the order in which contacts are broken during single molecule protein stretching experiments.
- Published in:
- Proteins, 2008, v. 71, n. 1, p. 45, doi. 10.1002/prot.21652
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- Article