Automating the amino acid identification in elliptical dichroism spectrometer with Machine Learning

Συγγραφείς: Ridhanya Sree Balamurugan, Yusuf Asad, Tommy Gao, Dharmakeerthi Nawarathna, Umamaheswara Rao Tida, Dali Sun

Πηγή: PLoS One
PLoS ONE, Vol 20, Iss 1, p e0317130 (2025)

Θεματικοί όροι: Light, Dichroism, Science, Medical Biochemistry, Circular dichroism, Biochemistry, Absorption, Machine Learning, Automation, Machine learning, Methods, Chomatographic analysis, Amino Acids, Mass spectrometry, Circular dichroism/methods, Theory and Algorithms, Circular Dichroism, Methodology, and Proteins, Pharmacy and Pharmaceutical Sciences, Mechanization, Amino acids, Medicine, Health aspects, Peptides, Algorithms, Research Article

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/39823430
https://doaj.org/article/6669965921f5422ba8c7811b387cde3a

Mass-resolved electronic circular dichroism ion spectroscopy

Συγγραφείς: Daly, Steven, Rosu, Frédéric Johanna R, Gabelica, Valérie

Πηγή: ISSN: 0036-8075 ; Science, vol. 368, no. 6498 (2020) p. 1465-1468.

Θεματικοί όροι: Circular Dichroism / methods, DNA / chemistry, Guanine / analysis, Guanine / chemistry, Mass Spectrometry / methods, Nucleic Acid Conformation, Top 10

Relation: info:eu-repo/semantics/altIdentifier/pmid/32587016; info:eu-repo/grantAgreement/EC/FP7/616551/EU/Advanced mass spectrometry approaches to reveal nucleic acid folding energy landscapes/DNAFOLDIMS; unige:182490

Διαθεσιμότητα: https://archive-ouverte.unige.ch/unige:182490

Protein-Containing PEGylated Cubosomic Particles: Freeze-Fracture Electron Microscopy and Synchrotron Radiation Circular Dichroism Study

Συγγραφείς: Angelov, Borislav, Angelova, Angelina, Papahadjopoulos-Sternberg, Brigitte, Hoffmann, Søren Vrønning, Nicolas, Valérie, Lesieur, Sylviane

Πηγή: The journal of physical chemistry / B 116, 3089-3093 (2005). doi:10.1021/jp303863q
Angelov, B, Angelova, A, Papahadjopoulos-Sternberg, B, Hoffmann, S V, Nicolas, V & Lesieur, S 2012, 'Protein-Containing PEGylated Cubosomic Particles: Freeze-Fracture Electron Microscopy and Synchrotron Radiation Circular Dichroism Study', Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, vol. 116, no. 26, pp. 7676-7686. https://doi.org/10.1021/jp303863q

Θεματικοί όροι: Nanoparticles: ultrastructure, Poloxamer, Chymotrypsinogen: chemistry, Circular Dichroism: methods, 01 natural sciences, Glycerides, Polyethylene Glycols, Nanoparticles: chemistry, Microscopy, Electron: methods, Glycerides: chemistry, Freeze Fracturing, Microscopy, Confocal, Freeze Fracturing: methods, Circular Dichroism, Water, Polyethylene Glycols: chemistry, Water: chemistry, 16. Peace & justice, Chymotrypsinogen, Liquid Crystals, 0104 chemical sciences, Microscopy, Electron, Liquid Crystals: chemistry, Nanoparticles, Poloxamer: chemistry, monoolein, Synchrotrons

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/22720820
https://pubs.acs.org/doi/abs/10.1021/jp303863q
https://www.ncbi.nlm.nih.gov/pubmed/22720820
http://pubs.acs.org/doi/abs/10.1021/jp303863q
https://pubs.acs.org/doi/10.1021/jp303863q
https://bib-pubdb1.desy.de/record/143948
https://pure.au.dk/portal/en/publications/9f9740c7-4cc3-4268-92f0-678019960178
https://doi.org/10.1021/jp303863q

Protein secondary structure content in solution, films and tissues: Redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra

Συγγραφείς: Goormaghtigh, Erik, Gasper, Régis, Benard, Audrey, Goldsztein, Andrea, Raussens, Vincent

Πηγή: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1794:1332-1343

Θεματικοί όροι: Male, 0301 basic medicine, Protein Structure, Secondary, Biopsy, Breast Neoplasms, Prostatic Neoplasms -- chemistry, Biosensing Techniques, Circular dichroism, Protein Structure, Secondary, Cell Line, FTIR imaging, 03 medical and health sciences, Circular Dichroism -- methods, Secondary structure, Cell Line, Tumor, Spectroscopy, Fourier Transform Infrared, Chimie, Humans, Spectroscopy, Protein film, 0303 health sciences, Tumor, Fourier Transform Infrared -- methods, FTIR sensors, Circular Dichroism, Prostatic Neoplasms, Proteins, Breast Neoplasms -- chemistry, IR spectroscopy, Female, Proteins -- analysis

Περιγραφή αρχείου: 2 full-text file(s): application/pdf; application/pdf

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/19540367
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/74181/Details
https://www.sciencedirect.com/science/article/pii/S1570963909001435
https://core.ac.uk/display/8872560
http://europepmc.org/abstract/MED/19540367
https://www.sciencedirect.com/science/article/abs/pii/S1570963909001435#!

Comparison of the Thermodynamics and Base-Pair Dynamics of a Full LNA:DNA Duplex and of the Isosequential DNA:DNA Duplex

Συγγραφείς: Bruylants, Gilles, Boccongelli, Marina, Snoussi, Karim, Bartik, Kristin

Πηγή: Biochemistry, 48 (35

Θεματικοί όροι: 0301 basic medicine, 0303 health sciences, Molecular Structure, Circular Dichroism, Nucleic Acid Heteroduplexes, Oligonucleotides, Nucleic Acid Hybridization, Chemical, DNA, Sciences de l'ingénieur, Oligonucleotides -- chemistry, Nucleic Acid Heteroduplexes -- chemistry, 03 medical and health sciences, Models, Chemical, Models, Circular Dichroism -- methods, DNA -- chemistry, Chimie, Nucleic Acid Conformation, Thermodynamics, Thermodynamique chimique, Base Pairing

Περιγραφή αρχείου: 2 full-text file(s): application/pdf; application/pdf

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/19670874
https://pubmed.ncbi.nlm.nih.gov/19670874/
https://www.ncbi.nlm.nih.gov/pubmed/19670874
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/54636/Details
https://pubs.acs.org/doi/abs/10.1021/bi900615z
https://dial.uclouvain.be/pr/boreal/object/boreal:35339
https://pubs.acs.org/doi/10.1021/bi900615z
http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/54636

Evidence for a dimeric assembly of two titin/telethonin complexes induced by the telethonin C-terminus

Συγγραφείς: Maxim V. Petoukhov, Matthias Wilmanns, Peijian Zou, Stephan Lange, Nikos Pinotsis, Dmitri I. Svergun, Mathias Gautel

Πηγή: Pinotsis, N, Petoukhov, M, Lange, S, Svergun, D, Zou, P, Gautel, M & Wilmanns, M 2006, ' Evidence for a dimeric assembly of two titin/telethonin complexes induced by the telethonin C-terminus ', Journal of Structural Biology, vol. 155, no. 2, pp. 239-50 . https://doi.org/10.1016/j.jsb.2006.03.028

Θεματικοί όροι: Circular Dichroism/methods, Crystallization/methods, 0301 basic medicine, Peptide Fragments/chemistry, Immunoblotting, Muscle Proteins, Protein Kinases/genetics, Crystallography, X-Ray, Protein Structure, Secondary, 03 medical and health sciences, Chlorocebus aethiops, Sarcomeres/metabolism, Animals, Humans, Connectin, Myocytes, Cardiac, Crystallography, X-Ray/methods, 0303 health sciences, Microscopy, Confocal/methods, Microscopy, Confocal, Circular Dichroism, Genetic Complementation Test, Muscle Proteins/chemistry, Myocytes, Cardiac/metabolism, Peptide Fragments, Protein Structure, Tertiary, Rats, COS Cells, Crystallization, Dimerization, Protein Kinases, Protein Binding

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/16713295
https://www.rcsb.org/structure/2F8V
https://www.ncbi.nlm.nih.gov/pubmed/16713295
https://core.ac.uk/display/1623969
http://www.rcsb.org/pdb/explore/explore.do?pdbId=2F8V
https://europepmc.org/abstract/MED/16713295
https://www.sciencedirect.com/science/article/pii/S1047847706001134

Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements

Συγγραφείς: Navea, Susana, Tauler, Romá, Goormaghtigh, Erik, de Juan, Anna

Πηγή: Proteins: Structure, Function, and Bioinformatics. 63:527-541

Θεματικοί όροι: 0301 basic medicine, Protein Structure, Secondary, 0303 health sciences, Crystallography, Spectrophotometry, Infrared, Protein Conformation, Circular Dichroism, Protein -- classification, Circular dichroism, Crystallography, X-Ray, Infrared -- methods, Protein Structure, Secondary, Protein classification, Databases, 03 medical and health sciences, Spectrophotometry, Circular Dichroism -- methods, Partial Least Squares (PLS), X-Ray, Chimie, Cluster Analysis, Chemometrics, Databases, Protein, Infrared spectroscopy

Περιγραφή αρχείου: 2 full-text file(s): application/pdf; application/pdf

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/16456850
https://pubmed.ncbi.nlm.nih.gov/16456850/
https://europepmc.org/article/MED/16456850
https://core.ac.uk/display/8872589
https://onlinelibrary.wiley.com/doi/10.1002/prot.20890/abstract
https://www.onlinelibrary.wiley.com/doi/abs/10.1002/prot.20890
http://www.ncbi.nlm.nih.gov/pubmed/16456850

Brassica juncea 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase 1: expression and characterization of recombinant wild-type and mutant enzymes

Συγγραφείς: Nagegowda, DA, Bach, TJ, Chye, ML

Πηγή: Biochemical Journal. 383:517-527

Θεματικοί όροι: Hydroxymethylglutaryl-CoA Synthase, 0301 basic medicine, Histidine - Biosynthesis - Chemistry - Metabolism, Cockroaches, Plant Proteins - Chemistry - Genetics, Lactones, Mice, Enzymologic - Genetics, Mutation - Genetics, Lactones - Metabolism, 0303 health sciences, Circular Dichroism, Fatty Acids, Acetyl-Coa Hydrolase - Metabolism, Temperature, Hydrogen-Ion Concentration, Schizosaccharomyces Pombe Proteins - Chemistry, Avian Proteins - Chemistry, Sequence Alignment - Methods, Fatty Acids, Unsaturated, Insect Proteins, Unsaturated - Metabolism, Molecular Sequence Data, Cockroaches - Genetics, Mustard Plant - Enzymology, Arginine, Acetyl-CoA Hydrolase, Gene Expression Regulation, Enzymologic, Cations - Metabolism, Fatty Acids, Unsaturated - Metabolism, Avian Proteins, 03 medical and health sciences, Insect Proteins - Chemistry, Cations, Chickens - Genetics, Animals, Humans, Histidine, Amino Acid Sequence, Hydroxymethylglutaryl-Coa Synthase - Biosynthesis - Chemistry - Genetics - Metabolism, Circular Dichroism - Methods, Arabidopsis Proteins, Arginine - Genetics, Arabidopsis Proteins - Chemistry, Recombinant Proteins - Metabolism, Gene Expression Regulation, Enzymologic - Genetics, Molecular Weight, Kinetics, Gene Expression Regulation, Chickens

Σύνδεσμος πρόσβασης: https://europepmc.org/articles/pmc1133745?pdf=render
https://pubmed.ncbi.nlm.nih.gov/15233626
https://hub.hku.hk/handle/10722/179341
https://portlandpress.com/biochemj/article/383/3/517/91544/Brassica-juncea-3-hydroxy-3-methylglutaryl-HMG-CoA
https://www.ncbi.nlm.nih.gov/pubmed/15233626
http://www.biochemj.org/content/383/3/517
http://europepmc.org/articles/PMC1133745
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1133745
http://hdl.handle.net/10722/179341

The optimization of protein secondary structure determination with infrared and circular dichroism spectra

Συγγραφείς: Oberg, KEITH, Ruysschaert, Jean Marie, Goormaghtigh, Erik

Πηγή: European Journal of Biochemistry. 271:2937-2948

Θεματικοί όροι: 0301 basic medicine, Protein Structure, Secondary, 0303 health sciences, Spectrophotometry, Infrared, Protein, Circular Dichroism, Proteins, Proteins -- chemistry, PLS, Circular dichroism, Sensitivity and Specificity, Infrared -- methods, Protein Structure, Secondary, Databases, 03 medical and health sciences, FTIR, Spectrophotometry, Circular Dichroism -- methods, Multivariate Analysis, Chimie, Protein secondary structure, Databases, Protein, Algorithms

Περιγραφή αρχείου: 1 full-text file(s): application/pdf

Σύνδεσμος πρόσβασης: https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/j.1432-1033.2004.04220.x
https://pubmed.ncbi.nlm.nih.gov/15233789
http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.2004.04220.x/full
http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.2004.04220.x/abstract
https://www.ncbi.nlm.nih.gov/pubmed/15233789
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/77577/Details
https://europepmc.org/abstract/MED/15233789
https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.2004.04220.x

Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis

Συγγραφείς: Oberg, KEITH, Ruysschaert, Jean Marie, Goormaghtigh, Erik

Πηγή: Protein Science. 12:2015-2031

Θεματικοί όροι: Proteomics, 0301 basic medicine, Protein Structure, Secondary, Spectrophotometry, Infrared, Protein Conformation, Statistics as Topic -- methods, Statistics as Topic, Circular dichroism, Proteomics -- methods, Crystallography, X-Ray, Mass Spectrometry, Protein Structure, Secondary, Databases, 03 medical and health sciences, Computational Biology -- methods, Circular Dichroism -- methods, Secondary structure, Spectroscopy, Fourier Transform Infrared, Methods, Chimie, Chemometrics, Infrared spectroscopy, Spectroscopy, 0303 health sciences, Crystallography, Fourier Transform Infrared -- methods, Data interpretation, Circular Dichroism, Proteins, Computational Biology, Peptides -- chemistry, Databases as Topic, Spectrophotometry, Statistical analysis, X-Ray, Basis sets, Infrared, protein, Peptides, Analysis, Software, Mass Spectrometry -- methods

Περιγραφή αρχείου: 2 full-text file(s): application/pdf; application/pdf

Σύνδεσμος πρόσβασης: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1110/ps.0354703
https://pubmed.ncbi.nlm.nih.gov/12931000
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/77590/Details
https://core.ac.uk/display/8875810
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323998
https://onlinelibrary.wiley.com/doi/full/10.1110/ps.0354703
http://europepmc.org/articles/PMC2323998

Protein concentration is not an absolute prerequisite for the determination of secondary structure from circular dichroism spectra: a new scaling method

Συγγραφείς: Raussens, Vincent, Ruysschaert, Jean Marie, Goormaghtigh, Erik

Πηγή: Analytical Biochemistry. 319:114-121

Θεματικοί όροι: 0301 basic medicine, Protein Structure, Secondary, 0303 health sciences, 03 medical and health sciences, Circular Dichroism -- methods, Circular Dichroism, Proteins -- pharmacology, Chimie, Proteins, Proteins -- chemistry, Sensitivity and Specificity, Protein Structure, Secondary

Περιγραφή αρχείου: 1 full-text file(s): application/pdf

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/12842114
https://www.sciencedirect.com/science/article/pii/S0003269703002859
https://www.ncbi.nlm.nih.gov/pubmed/12842114
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/77591/Details
https://europepmc.org/article/MED/12842114

Calculation of K-edge circular dichroism of amino acids: Comparison of random phase approximation with other methods

Συγγραφείς: Kimberg, Victor, Kosugi, Nobuhiro

Πηγή: Journal of Chemical Physics. 126(24)

Θεματικοί όροι: Amino Acids, Amino Acids: chemistry, Anisotropy, Biophysics, Biophysics: methods, Chemical, Chemistry, Circular Dichroism, Circular Dichroism: methods, Entropy, Models, Molecular, Molecular Conformation, Oscillometry, Oxygen, Oxygen: chemistry, Photons, Physical, Physical: methods, Statistical, Thermodynamics, X-Rays

Περιγραφή αρχείου: print

Σύνδεσμος πρόσβασης: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-182317

The α-helical content of the transmembrane domain of the British dementia protein-2 (Bri2) determines its processing by signal peptide peptidase-like 2b (SPPL2b).

Συγγραφείς: Fluhrer, Regina, Martin, Lucas, Klier, Bärbel, Haug-Kröper, Martina, Grammer, Gudula, Nuscher, Brigitte, Haass, Christian

Πηγή: The journal of biological chemistry 287(7), 5156-5163 (2011). doi:10.1074/jbc.M111.328104

Θεματικοί όροι: info:eu-repo/classification/ddc/540, ADAM Proteins: genetics, ADAM Proteins: metabolism, ADAM10 Protein, Amino Acid Motifs, Amyloid Precursor Protein Secretases: genetics, Amyloid Precursor Protein Secretases: metabolism, Aspartic Acid Endopeptidases: genetics, Aspartic Acid Endopeptidases: metabolism, Circular Dichroism: methods, HEK293 Cells, Humans, Membrane Glycoproteins, Membrane Proteins: genetics, Membrane Proteins: metabolism, Mutagenesis, Protein Structure, Tertiary, Proteolysis, ITM2B protein, human, Membrane Proteins, Amyloid Precursor Protein Secretases, Aspartic Acid Endopeptidases, SPPL2b protein, ADAM Proteins

Θέμα γεωγραφικό: DE

Relation: info:eu-repo/semantics/altIdentifier/pmid/pmid:22194595; info:eu-repo/semantics/altIdentifier/issn/0021-9258; info:eu-repo/semantics/altIdentifier/issn/1067-8816; info:eu-repo/semantics/altIdentifier/issn/1083-351X; https://pub.dzne.de/record/136438

Διαθεσιμότητα: https://pub.dzne.de/record/136438
https://pub.dzne.de/search?p=id:%22DZNE-2020-02760%22

Imaging the in-plane magnetization in a Co microstructure by Fourier transform holography

Συγγραφείς: Tieg, C., Frömter, R., Stickler, D., Hankemeier, S., Kobs, A., Streit-Nierobisch, S., Gutt, C., Grübel, G., Oepen, H. P.

Πηγή: Optics express 18, 27251 (2010). doi:10.1364/OE.18.027251

Θεματικοί όροι: Circular Dichroism, Holography, Circular Dichroism: instrumentation, Magnetics: instrumentation, Cobalt, Equipment Design, 02 engineering and technology, Circular Dichroism: methods, Equipment Failure Analysis, Magnetics, Cobalt: chemistry, Holography: methods, Holography: instrumentation, 0210 nano-technology, Algorithms

Σύνδεσμος πρόσβασης: https://pubmed.ncbi.nlm.nih.gov/21197002
https://europepmc.org/article/MED/21197002
https://www.osapublishing.org/oe/abstract.cfm?uri=oe-18-26-27251
https://www.ncbi.nlm.nih.gov/pubmed/21197002
http://ui.adsabs.harvard.edu/abs/2010OExpr..1827251T/abstract
https://bib-pubdb1.desy.de/record/88682

Protein-Containing PEGylated Cubosomic Particles: Freeze-Fracture Electron Microscopy and Synchrotron Radiation Circular Dichroism Study

Συγγραφείς: Angelov, B., Angelova, A., Papahadjopoulos-Sternberg, B., Hoffmann, S. V., Nicolas, V., Lesieur, S.

Πηγή: The journal of physical chemistry / B 116, 3089-3093 (2005). doi:10.1021/jp303863q

Θεματικοί όροι: info:eu-repo/classification/ddc/530, Chymotrypsinogen: chemistry, Circular Dichroism: methods, Freeze Fracturing: methods, Glycerides: chemistry, Liquid Crystals: chemistry, Microscopy, Confocal, Electron: methods, Nanoparticles: chemistry, Nanoparticles: ultrastructure, Poloxamer: chemistry, Polyethylene Glycols: chemistry, Synchrotrons, Water: chemistry, Glycerides, Polyethylene Glycols, Poloxamer, monoolein, Water, Chymotrypsinogen

Θέμα γεωγραφικό: DE

Relation: info:eu-repo/semantics/altIdentifier/issn/1520-6106; info:eu-repo/semantics/altIdentifier/issn/1089-5647; info:eu-repo/semantics/altIdentifier/pmid/pmid:22720820; info:eu-repo/semantics/altIdentifier/wos/WOS:000305933800009; info:eu-repo/semantics/altIdentifier/issn/1520-5207

Διαθεσιμότητα: https://bib-pubdb1.desy.de/record/143948
https://bib-pubdb1.desy.de/search?p=id:%22PHPPUBDB-25662%22