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AMS 4.0: consensus prediction of post-translational modifications in protein sequences

Dariusz Plewczynski, Subhadip Basu, Indrajit Saha
2012 Amino Acids  
The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted  ...  Keywords Post-translational modifications Á AMS-4 Á High quality indices Á MLP Á Consensus Background Post-translational modification (PTM) is a chemical modification of a protein after its translation  ...  Acknowledgments SB is thankful to the Centre for Microprocessor Applications for Training Education and Research (CMATER) and PURSE project of Computer Science and Engineering Department, Jadavpur University  ... 
doi:10.1007/s00726-012-1290-2 pmid:22555647 pmcid:PMC3397139 fatcat:aulz6lihjrbydmbxqrqztlvjrq

Does Amount of Protein in Formula Matter for Low-Birthweight Infants? A Cochrane Systematic Review

Shahirose Premji, Tanis Fenton, Reg Sauve
2006 JPEN - Journal of Parenteral and Enteral Nutrition  
Results: A meta-analysis of 5 ran- domized trials indicated improved weight gain (weighted Protein is an important component of adequate nutrition because it provides essential amino acids required for  ...  We therefore per- formed a systematic review of the literature to deter- mine whether high (=3.0 g/kg/d but <4.0 g/kg/d) vs low (<3.0 g/kg/d) or very high protein intakes (=4.0 g/kg/d) during the initial  ... 
doi:10.1177/0148607106030006507 pmid:17047176 fatcat:azo2xtra2vbfjawkas45oa6vy4

Variants at HLA-A , HLA-C , and HLA-DQB1 Confer Risk of Psoriasis Vulgaris in Japanese

Jun Hirata, Tomomitsu Hirota, Takeshi Ozeki, Masahiro Kanai, Takeaki Sudo, Toshihiro Tanaka, Nobuyuki Hizawa, Hidemi Nakagawa, Shinichi Sato, Taisei Mushiroda, Hidehisa Saeki, Mayumi Tamari (+1 others)
2018 Journal of Investigative Dermatology  
We note that our large-scale imputation reference panel achieved high imputation quality of HLA-C*06:02 despite its low frequency (Rsq ¼ 0.91).  ...  HLA amino acid positions with psoriasis vulgaris risk in HLA-A and HLA-DQ molecules are indicated in three-dimensional ribbon models.  ...  HS and MT were supported by a grant from the Ministry of Education, Culture, Sports, Science and Technology. JH is an employee of Teijin Pharma Limited.  ... 
doi:10.1016/j.jid.2017.10.001 pmid:29031612 fatcat:r344x2sq2vfdpkgjokbhqzxhx4

Modelling structural constraints on protein evolution via side-chain conformational states: Supplementary files [article]

Umberto Perron, Alexey M Kozlov, Alexandros Stamatakis, Nick Goldman, Iain Moal
2019 bioRxiv   pre-print
of amino acids depend strongly upon side-chain geometry.  ...  Each character specifies an amino acid as well a rotamer state: the discrete geometric pattern of permitted side-chain atomic positions.  ...  In this paper we apply our model to empirical data where both amino acid 318 sequences and the corresponding high-quality atomic coordinates.  ... 
doi:10.1101/530634 fatcat:nb3b75ibzjadrpmay7bpjvcbay

In ovo feeding technology: Embryonic development, Hatchability and Hatching quality of broiler chicks

2021 Turk veterinerlik ve hayvancilik dergisi  
3 This study reviewed the effects of in ovo feeding application on incubation performance and chick 4 quality in broilers.  ...  Effectiveness of incubation and chick quality in commercial chicken broiler 5 production have a decisive role in production cost as well as efficiency and are a prerequisite for 6 sustainable production  ...  It was observed that hatchability decreased in eggs injected with amino acid 4 using a 19 mm needle compared to a 13 mm needle and, the bodyweight relative to before 5 incubation egg weight of the chicks  ... 
doi:10.3906/vet-2006-20 fatcat:pogdzq27vnh7jhzwbowzxggheu

Detection and Mapping of Haemoglobin variants in blood fingermarks by MALDI MS for suspect "profiling"

Cameron Heaton, Matthias Witt, Laura M Cole, Jason Eyre, Simon Tazzyman, Richard McColm, Simona Francese
2021 The Analyst  
Over the past seven years Matrix Assisted Laser Desorption Ionisation Mass Spectrometry Profiling (MALDI MSP) and Imaging (MALDI MSI) have proven to be feasible tools for the detection of blood...  ...  The red font indicates the amino acid mutation. Analyst Accepted ManuscriptOpen Access Article. Published on 07 June 2021. Downloaded on 6/9/2021 7:19:35 AM.  ...  This variant arises from a substitution of a glutamic acid for a glutamine at the 22 nd amino acid position in the β globin chain (β22 Glu→Lys).  ... 
doi:10.1039/d1an00578b pmid:34105523 fatcat:vfpmwwe6rbexpi5qauo2wn4l5u

Predicting protein secondary structure with Neural Machine Translation [article]

Evan Weissburg, Ian Bulovic
2021 arXiv   pre-print
We hypothesize that Neural Machine Translation can improve upon current predictive accuracy by better encoding complex relationships between nearby but non-adjacent amino acids.  ...  We overview our modifications to the framework in order to improve accuracy on protein sequences. We report 65.9% Q3 accuracy and analyze the strengths and weaknesses of our predictive model.  ...  The authors declare no conflicts of interest.  ... 
arXiv:1809.09210v2 fatcat:rmlmltrzlrgtlbtb2c65azcdaa

Progress on Nutrient Composition, Meat Standardization, Grading, Processing, and Safety for Different Types of Meat Sources

Nelson Huerta-Leidenz
2021 Foods  
Beef contains a plethora of healthy nutrients and it is the highest valued livestock-based food product [...]  ...  I am also grateful to Nuria Prieto, Alexandra Calle, Caterina Rufo, Manuel Juarez, and Oscar Lopez Campos for their assistance in proofreading the excerpts of their own articles.  ...  Finally, I would like to recognize the valuable help that I received from Tania Ngapo for editing the last version of the manuscript.  ... 
doi:10.3390/foods10092128 pmid:34574238 fatcat:pesbupj6zzc5tnqxjshtfqpw2u

Use of spent coffee grounds as food ingredient in bakery products

Nuria Martinez-Saez, Alba Tamargo García, Inés Domínguez Pérez, Miguel Rebollo-Hernanz, Marta Mesías, Francisco J. Morales, María A. Martín-Cabrejas, Maria Dolores del Castillo
2017 Food Chemistry  
The present research aimed to evaluate the use of spent coffee grounds (SCG) from instant coffee as a food ingredient and its application in bakery products.  ...  Innovative biscuits were obtained according to consumers' preferences with high nutritional and sensorial quality and potential to reduce the risk of chronic diseases such as obesity and diabetes.  ...  The present research is part of the PhD. Thesis of Martinez-Saez, N. FPI-predoc fellow belongs to Autonomous University of Madrid (UAM), Spain.  ... 
doi:10.1016/j.foodchem.2016.07.173 pmid:27596399 fatcat:xbppbl53pra7tfiksdh56musse

International Society of Sports Nutrition Position Stand: protein and exercise

Ralf Jäger, Chad M. Kerksick, Bill I. Campbell, Paul J. Cribb, Shawn D. Wells, Tim M. Skwiat, Martin Purpura, Tim N. Ziegenfuss, Arny A. Ferrando, Shawn M. Arent, Abbie E. Smith-Ryan, Jeffrey R. Stout (+10 others)
2017 Journal of the International Society of Sports Nutrition  
We would like to thank all the participants and researchers who contributed to the research studies and reviews described in this position stand.  ...  Results indicated that peptide hydrolysates produced a faster increase in venous plasma amino acids compared to milk proteins.  ...  Beyond amino acid content, the fat, calorie, and micronutrient content, and presence of various bioactive peptides all contribute to a protein's quality.  ... 
doi:10.1186/s12970-017-0177-8 pmid:28642676 pmcid:PMC5477153 fatcat:rr335ptbdzh6rkzxp572qrtbsu

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement [article]

Aleksandra Badaczewska-Dawid, Sebastian Kmiecik, Michal Kolinski
2020 bioRxiv   pre-print
These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy  ...  Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction  ...  Acknowledgments This work was supported by the National Science Centre of Poland, grant MAESTRO no. 2014/14/A/ST6/00088.  ... 
doi:10.1101/2020.03.21.001396 fatcat:poruk753xrfmpmhbgk57ucyr6i

Computing Bayes Factors Using Thermodynamic Integration

Nicolas Lartillot, Hervé Philippe, Paul Lewis
2006 Systematic Biology  
Finally, we apply our method to the comparison of several alternative models of amino-acid replacement.  ...  In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods.  ...  ACKNOWLEDGMENTS We wish to thank Henner Brinkmann for making available the aligned sequences on which this work was based.  ... 
doi:10.1080/10635150500433722 pmid:16522570 fatcat:iw6dunyexrcxxdso7pvqeakyoe

Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors

Anja Mösch, Silke Raffegerst, Manon Weis, Dolores J. Schendel, Dmitrij Frishman
2019 Frontiers in Genetics  
application of machine learning methods inevitable.  ...  Particularly, potential cross-reactivity is a major consideration since off-target toxicity can pose a major threat to patient safety.  ...  amino acids.  ... 
doi:10.3389/fgene.2019.01141 pmid:31798635 pmcid:PMC6878726 fatcat:zsyif2i62vfljnp3rtv3lbr7cm

Chemical Composition of Pinus nigra Arn. Unripe Seeds from Bulgaria

Hafize Fidan, Stanko Stankov, Magdalena Stoyanova, Zhana Petkova, Nadezhda Petkova, Albena Stoyanova, Sezai Ercisli, Ravish Choudhary, Rohini Karunakaran
2022 Plants  
The amount of unsaturated pinolenic (10.5%) and oleic acids (8.8%) was also rather high. The amino acid composition of the protein fraction of seedcakes was also determined.  ...  The present paper aims to investigate the chemical composition of unripe black pine seeds obtained from Bulgaria.  ...  The oleic acid content was lower (8.8%), followed by a small quantity of linolenic acid (3.0%).  ... 
doi:10.3390/plants11030245 pmid:35161225 pmcid:PMC8840165 fatcat:krfl57smwvatzga55sw4r5o3i4

Dietary Intake of Branched Chain Amino Acids and Breast Cancer Risk in the NHS and NHS II Prospective Cohorts

Deirdre Tobias, Boyang Chai, Rulla M Tamimi, JoAnn E Manson, Frank B Hu, Walter C Willett, A Heather Eliassen
2021 JNCI Cancer Spectrum  
Background Branched-chain amino acids (BCAAs) are essential amino acids common throughout the US diet.  ...  Results We observed 10,046 incident cases of breast cancer over a median of 20.8 years of follow-up.  ...  Acknowledgements: We would like to thank the participants and staff of the Nurses' Health Studies for their valuable contributions as well as the following state cancer Downloaded from https://academic.oup.com  ... 
doi:10.1093/jncics/pkab032 pmid:34632269 pmcid:PMC8494188 fatcat:jimojcgmqjb43klf2ty2sr5dbq
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