scholarly journals Efficient Amino Acid Conformer Search with Bayesian Optimization

2021 ◽  
Author(s):  
Lincan Fang ◽  
Esko Makkonen ◽  
Milica Todorović ◽  
Patrick Rinke ◽  
Xi Chen
Keyword(s):  
Amino Acid ◽  
Bayesian Optimization

scholarly journals Succinylation Site Prediction Based on Protein Sequences Using the IFS-LightGBM (BO) Model

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Lu Zhang ◽  
Min Liu ◽  
Xinyi Qin ◽  
Guangzhong Liu
Keyword(s):  
Feature Selection ◽  
Amino Acid ◽  
Optimization Algorithm ◽  
Feature Selection Method ◽  
Selection Method ◽  
Bayesian Optimization ◽  
Feature Subset ◽  
Bayesian Optimization Algorithm ◽  
Incremental Feature Selection ◽  
Optimal Feature Subset

Succinylation is an important posttranslational modification of proteins, which plays a key role in protein conformation regulation and cellular function control. Many studies have shown that succinylation modification on protein lysine residue is closely related to the occurrence of many diseases. To understand the mechanism of succinylation profoundly, it is necessary to identify succinylation sites in proteins accurately. In this study, we develop a new model, IFS-LightGBM (BO), which utilizes the incremental feature selection (IFS) method, the LightGBM feature selection method, the Bayesian optimization algorithm, and the LightGBM classifier, to predict succinylation sites in proteins. Specifically, pseudo amino acid composition (PseAAC), position-specific scoring matrix (PSSM), disorder status, and Composition of k -spaced Amino Acid Pairs (CKSAAP) are firstly employed to extract feature information. Then, utilizing the combination of the LightGBM feature selection method and the incremental feature selection (IFS) method selects the optimal feature subset for the LightGBM classifier. Finally, to increase prediction accuracy and reduce the computation load, the Bayesian optimization algorithm is used to optimize the parameters of the LightGBM classifier. The results reveal that the IFS-LightGBM (BO)-based prediction model performs better when it is evaluated by some common metrics, such as accuracy, recall, precision, Matthews Correlation Coefficient (MCC), and F -measure.

The staining pattern of the tropomyosin sequence is displayed in a new paracrystal

1986 ◽  
Vol 44 ◽  
pp. 150-151
Author(s):  
M.K. Lamvik ◽  
L.L. Klatt
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Staining Pattern ◽  
Banding Patterns ◽  
Mass Thickness ◽  
New Form

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.

Electron probe x-ray microanalysis and electron microscopy of amino acid absorption and transport by the small intestine: inhibition by chemical poisons and correlation to the elemental composition of the epithelial cells

1986 ◽  
Vol 44 ◽  
pp. 134-135
Author(s):  
A. J. Tousimis
Keyword(s):  
Small Intestine ◽  
Amino Acid ◽  
Epithelial Cells ◽  
Elemental Composition ◽  
Isotope Labeling ◽  
Structural Components ◽  
X Ray ◽  
Human Small Intestine ◽  
Transport Studies

The elemental composition of amino acids is similar to that of the major structural components of the epithelial cells of the small intestine and other tissues. Therefore, their subcellular localization and concentration measurements are not possible by x-ray microanalysis. Radioactive isotope labeling: I131-tyrosine, Se75-methionine and S35-methionine have been successfully employed in numerous absorption and transport studies. The latter two have been utilized both in vitro and vivo, with similar results in the hamster and human small intestine. Non-radioactive Selenomethionine, since its absorption/transport behavior is assumed to be the same as that of Se75- methionine and S75-methionine could serve as a compound tracer for this amino acid.

Immunoelectron microscope detection of C-type natriuretic peptide in normal human atrial tissue

1993 ◽  
Vol 51 ◽  
pp. 388-389
Author(s):  
Chi-Ming Wei ◽  
Margaret Hukee ◽  
Christopher G.A. McGregor ◽  
John C. Burnett
Keyword(s):  
Amino Acid ◽  
Natriuretic Peptide ◽  
Vascular Tone ◽  
Cardiac Tissue ◽  
Ring Structure ◽  
Terminal Amino Acid ◽  
Amino Acid Peptide ◽  
Normal Human ◽  
Terminal Amino ◽  
The Brain

C-type natriuretic peptide (CNP) is a newly identified peptide that is structurally related to atrial (ANP) and brain natriuretic peptide (BNP). CNP exists as a 22-amino acid peptide and like ANP and BNP has a 17-amino acid ring formed by a disulfide bond. Unlike these two previously identified cardiac peptides, CNP lacks the COOH-terminal amino acid extension from the ring structure. ANP, BNP and CNP decrease cardiac preload, but unlike ANP and BNP, CNP is not natriuretic. While ANP and BNP have been localized to the heart, recent investigations have failed to detect CNP mRNA in the myocardium although small concentrations of CNP are detectable in the porcine myocardium. While originally localized to the brain, recent investigations have localized CNP to endothelial cells consistent with a paracrine role for CNP in the control of vascular tone. While CNP has been detected in cardiac tissue by radioimmunoassay, no studies have demonstrated CNP localization in normal human heart by immunoelectron microscopy.

Amino Acid Metabolism

1979 ◽  
Vol 7 (1) ◽  
pp. 261-262
Author(s):  
E. V. ROWSELL
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism

Increased expression of an amino acid transporter LAT1 in healing of acetic acid-induced chronic gastric ulcer in rats

2001 ◽  
Vol 120 (5) ◽  
pp. A153-A153
Author(s):  
S MIYAMOTO ◽  
K KATO ◽  
Y ISHII ◽  
S ASAI ◽  
T NAGAISHI ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Gastric Ulcer ◽  
Amino Acid ◽  
Amino Acid Transporter ◽  
Chronic Gastric Ulcer ◽  
Acid Transporter

Amino Acid Excretion in Patients With Gastro Intestinal Disease During Ingestion of Various Protein Supplements

1950 ◽  
Vol 16 (4) ◽  
pp. 757-763 ◽  
Author(s):  
A. Leonard Sheffner ◽  
Joseph B. Kirsner ◽  
Walter L. Palmer
Keyword(s):  
Amino Acid ◽  
Intestinal Disease ◽  
Acid Excretion ◽  
Protein Supplements

Amino Acid Cleanser

2009 ◽  
Vol 40 (11) ◽  
pp. 42-42
Keyword(s):  
Amino Acid
Sign in / Sign up

Export Citation Format

Share Document