KnotProt: A database of proteins with knots and slipknots
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KnotProt: A database of proteins with knots and slipknots
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
KnotProt
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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KnotProt: A database of proteins with knots and slipknots
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
KnotProt
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
KnotProt: A database of proteins with knots and slipknots
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
KnotProt
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The database presents extensive information about the biological function of proteins with non-trivial knotting and enables users to analyze new structures.
Description
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KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The database presents extensive information about the biological function of proteins with non-trivial knotting and enables users to analyze new structures.
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Proteins with Topological knots and slipknots
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://knotprot.cent.uw.edu.pl/Webpage
More detailed information about this field from each metasource.
http://knotprot.cent.uw.edu.pl/
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://biocomp.chem.uw.edu.pl/protop/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
Conservation of complex knotting and slipknotting patterns in proteins
PMID: 22685208
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku1059
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Conservation of complex knotting and slipknotting patterns in proteins
PMID: 22685208
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku1059
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Conservation of complex knotting and slipknotting patterns in proteins
PubMed citations: 75.
75 articles citing: Conservation of complex knotting and slipknotting patterns in proteins
AlphaFold predicts the most complex protein knot and composite protein knots. PMID:35900026
The Local Topological Free Energy of the SARS-CoV-2 Spike Protein. PMID:35893978
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. PMID:35609987
The protein folding rate and the geometry and topology of the native state. PMID:35430582
Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics. PMID:35357594
Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. PMID:35187078
Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations. PMID:35136085
Lasso Proteins-Unifying Cysteine Knots and Miniproteins. PMID:34833285
Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. PMID:34827686
Ubiquitin carboxyl-terminal hydrolase L-1 in brain: Focus on its oxidative/nitrosative modification and role in brains of subjects with Alzheimer disease and mild cognitive impairment. PMID:34737037
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PMID:34648493
"Protein" no longer means what it used to. PMID:34308370
Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. PMID:34163946
SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment. PMID:33921228
On topology and knotty entanglement in protein folding. PMID:33439862
Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. PMID:33028204
GLN: a method to reveal unique properties of lasso type topology in proteins. PMID:32938999
Topoly: Python package to analyze topology of polymers. PMID:32935829
Knot polynomials of open and closed curves. PMID:32922152
Mg2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study. PMID:32904895
GISA: using Gauss Integrals to identify rare conformations in protein structures. PMID:32566389
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. PMID:32453784
Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data. PMID:32023061
Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures. PMID:31892272
Chromatin Is Frequently Unknotted at the Megabase Scale. PMID:31818464
Defining and detecting links in chromosomes. PMID:31409805
Searching the Optimal Folding Routes of a Complex Lasso Protein. PMID:31235180
Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding. PMID:31182755
Topological descriptions of protein folding. PMID:31000594
To Tie or Not to Tie? That Is the Question. PMID:30965758
Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. PMID:30965745
Ubiquitin C-terminal hydrolase L1 (UCH-L1) loss causes neurodegeneration by altering protein turnover in the first postnatal weeks. PMID:30923110
Effects of knot tightness at the molecular level. PMID:30683725
KnotProt 2.0: a database of proteins with knots and other entangled structures. PMID:30508159
Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations. PMID:30314655
KnotGenome: a server to analyze entanglements of chromosomes. PMID:29905836
The exclusive effects of chaperonin on the behavior of proteins with 52 knot. PMID:29547629
Studies of global and local entanglements of individual protein chains using the concept of knotoids. PMID:28740166
TrmD: A Methyl Transferase for tRNA Methylation With m1G37. PMID:28601227
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume. PMID:28489858
Molecular Knots. PMID:28477423
Synthesizing topological structures containing RNA. PMID:28361879
Pore translocation of knotted DNA rings. PMID:28351979
Topological knots and links in proteins. PMID:28280100
Proteins analysed as virtual knots. PMID:28205562
Topological transformations in proteins: effects of heating and proximity of an interface. PMID:28051124
Characterization of the Folding of a 52-Knotted Protein Using Engineered Single-Tryptophan Variants. PMID:28002735
Complex lasso: new entangled motifs in proteins. PMID:27874096
In Search of Functional Advantages of Knots in Proteins. PMID:27806097
LinkProt: a database collecting information about biological links. PMID:27794552
Folding analysis of the most complex Stevedore's protein knot. PMID:27527519
Ubiquitin C-terminal hydrolase L1 (UCH-L1): structure, distribution and roles in brain function and dysfunction. PMID:27515257
Knotting and unknotting of a protein in single molecule experiments. PMID:27339135
LassoProt: server to analyze biopolymers with lassos. PMID:27131383
Untangling the Influence of a Protein Knot on Folding. PMID:26958882
Design principles for rapid folding of knotted DNA nanostructures. PMID:26887681
The elusive quest for RNA knots. PMID:26828280
An Exploration of the Universe of Polyglutamine Structures. PMID:26495838
Knotted proteins: A tangled tale of Structural Biology. PMID:26380658
Subknots in ideal knots, random knots, and knotted proteins. PMID:25753957
Absence of knots in known RNA structures. PMID:25646433
KnotProt: a database of proteins with knots and slipknots. PMID:25361973
An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1. PMID:25331888
The ubiquitin C-terminal hydrolase L1 (UCH-L1) C terminus plays a key role in protein stability, but its farnesylation is not required for membrane association in primary neurons. PMID:25326379
The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations. PMID:24970203
Pierced Lasso Bundles are a new class of knot-like motifs. PMID:24945798
A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome. PMID:24628916
Shedding light on protein folding landscapes by single-molecule fluorescence. PMID:24336839
Protein folding on the ribosome studied using NMR spectroscopy. PMID:24083462
Effects of knots on protein folding properties. PMID:24023962
Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. PMID:23525263
Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways. PMID:23365638
How difficult is it to fold a knotted protein? In silico insights from surface-tethered folding experiments. PMID:23284997
Energy landscape of knotted protein folding. PMID:22891304 - http://dx.doi.org/10.1093/nar/gku1059
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protein
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
databases of individual protein families
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: KnotProt; KnotProt: A database of proteins with knots and slipknots; DOI: https://doi.org/10.25504/FAIRsharing.f5b5j1; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
databases of individual protein families
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure protein sequence protein family
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