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SCit: web tools for protein side chain conformation analysis

R. Gautier, A.-C. Camproux, P. Tuffery
2004 Nucleic Acids Research  
SCit is a web server providing services for protein side chain conformation analysis and side chain positioning.  ...  Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely  ...  Chomilier for suggesting the integration of our collection of tools related to side chains. This work  ... 
doi:10.1093/nar/gkh388 pmid:15215438 pmcid:PMC441526 fatcat:n6zzrgbwafhrdkpquj3u5hoesy

RPBS: a web resource for structural bioinformatics

C. Alland, F. Moreews, D. Boens, M. Carpentier, S. Chiusa, M. Lonquety, N. Renault, Y. Wong, H. Cantalloube, J. Chomilier, J. Hochez, J. Pothier (+3 others)
2005 Nucleic Acids Research  
As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling.  ...  Funding to pay the Open Access publication charges for this article was provided by INSERM.  ...  Other RPBS tools deal directly with 3D structures, such as SA-Search for finding structural similarities based on a structural alphabet (6) and Scit for comparing side chain conformations (7) .  ... 
doi:10.1093/nar/gki477 pmid:15980507 pmcid:PMC1160237 fatcat:22ndjqozljgjbb2oita5jcxpbq

Allergen Immunotherapy: Current and Future Trends

Gandhi F. Pavón-Romero, Maria Itzel Parra-Vargas, Fernando Ramírez-Jiménez, Esmeralda Melgoza-Ruiz, Nancy H. Serrano-Pérez, Luis M. Teran
2022 Cells  
These modified allergens induce clinical-immunological effects similar to those mentioned above, increasing the tolerance to other related allergens but with fewer side effects.  ...  Allergen immunotherapy (AIT) is the sole disease-modifying treatment for allergic rhinitis; it prevents rhinitis from progressing to asthma and lowers medication use.  ...  Indeed, proteomics applications include in vitro diagnostics, allergen discovery, and the analysis of biologicals proposed for AIT [190, 191] .  ... 
doi:10.3390/cells11020212 pmid:35053328 pmcid:PMC8774202 fatcat:xr3czkdlwbairmol2wnlztb62y

Blind men and elephants: What do citation summaries tell us about a research article?

Aaron Elkiss, Siwei Shen, Anthony Fader, Güneş Erkan, David States, Dragomir Radev
2007 Journal of the American Society for Information Science and Technology  
A citation summary is the set of citing sentences for a given article and can be used as a surrogate for the actual article in a variety of scenarios.  ...  Although T7-based approaches for amplification of mRNA have been described [14][15][16][17], these rely on the 3' polyA tails for priming and incorporation of the T7 promoter.  ...  SCit is a web server providing services for protein side chain conformation analysis and side chain positioning.  ... 
doi:10.1002/asi.20707 fatcat:qag4dzsinfe27edhmomzfxohay

Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features

Irene Righetto, Adelaide Milani, Giovanni Cattoli, Francesco Filippini
2014 BMC Bioinformatics  
Current analyses of viral evolution are based on serological and primary sequence comparison; however, comparative structural analysis of capsidic proteins can provide functional insights on surface regions  ...  However, viral evolution and spreading is strongly influenced by immunogenic features and capacity to bind host cells, depending in turn on the two major capsidic proteins.  ...  Given that distribution of surface charge is strongly influenced by the orientation of side chains, models refinement was performed using a number of tools based on different algorithms: SCWRL [35, 36  ... 
doi:10.1186/s12859-014-0363-5 pmid:25492298 pmcid:PMC4265342 fatcat:5lt2vc5k75h37kh7g4du2g66ye

Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate

B. R. Crane
1998 Science  
geiotype were obtaned by cell sortng a i d simulated for 8 hours w~th C o i A (5 p.g/ml) before preparatoi of a cytospi.  ...  nitric oxide (NO), which ronal NOS (nNOS, NOS1) and endotheliis a key intercellular signal and defensive a1 NOS (eNOS, NOS3) Produce low N O cytotoxin in the nerL70us, muscular, cardio-concentrations for  ...  The goal of the analysis presented here otherwise regulated is a common tool for species conservation.  ... 
doi:10.1126/science.279.5359.2121 pmid:9516116 fatcat:j4voskxz7jfz3prkv4aziu3crq

Local Protein Structures

Bernard Offmann, Manoj Tyagi, Akexandre de Brevern
2007 Current Bioinformatics  
They have also been used to predict the protein backbone conformation and in ab initio / de novo methods.  ...  Structural alphabets have been used to approximate and analyze local protein structures and to predict backbone conformation. This paper is divided in two parts.  ...  One application of this structural alphabet has been the web server SCit that allows analysing the protein side chain conformation [315] .  ... 
doi:10.2174/157489307781662105 fatcat:wosaroff5jhcnojc7zlozpvd5e

Krit 1 interactions with microtubules and membranes are regulated by Rap1 and integrin cytoplasmic domain associated protein-1

Sophie Béraud-Dufour, Romain Gautier, Corinne Albiges-Rizo, Pierre Chardin, Eva Faurobert
2007 The FEBS Journal  
We show that, like other FERM proteins, Krit1 adopts two conformations: a closed conformation in which its N-terminal NPAY motif interacts with its C-terminus and an opened conformation bound to ICAP-1  ...  As evidence suggests a role for Krit1 in Rap1-dependent pathways, we readdressed this question. Here, we demonstrate by biochemical assays that Krit1 is a specific Rap1 effector.  ...  ACKNOWLEDGEMENTS We are thankful to Frédéric Brau for excellent technical support in confocal microscopy. We  ... 
doi:10.1111/j.1742-4658.2007.06068.x pmid:17916086 pmcid:PMC2580780 fatcat:66n26qxwnbgcpf4cv5wcwfkqpm

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

Agnieszka Krzemińska, Vicent Moliner, Katarzyna Świderek
2016 Journal of the American Chemical Society  
The role of the protein dynamic was studied by protein isotope labelling in the framework of the Variational Transition State Theory.  ...  On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction.  ...  The position of the peptide in the active site was based on the arrangement with LP-130, and was build using Discovery Studio program version 3.5. 57 Using SCit tool developed by Tufféry and co-workers  ... 
doi:10.1021/jacs.6b06856 pmid:27935692 pmcid:PMC5178878 fatcat:xdlhjr2645cwndwktoiujhgi3u

Proceedings of the Canadian Society of Allergy and Clinical Immunology Annual Scientific Meeting 2020

2021 Allergy, Asthma & Clinical Immunology  
We identified 10 hot spot census tracts each for pediatric asthma ED visit and re-visit rates.  ...  Methods: We performed a single centre retrospective cohort study of children ages 1-17 with one or more ED visits for asthma at the Children's Hospital of Eastern Ontario.  ...  analysis.  ... 
doi:10.1186/s13223-021-00519-4 pmid:33785055 fatcat:twbwrkposjal7hhut2oy5ebkle

Sedentary behaviour as a risk factor for cardiovascular diseases in pediatric age

Chiara Mameli, Valentina Fabiano, Gian Vincenzo Zuccotti
2014 Italian Journal of Pediatrics  
The first pneumococcal conjugate vaccine (PCV7) included 7 serotypes and was licensed for the use in infants and in children < 5 years.  ...  Recently, preparations containing a greater number of pneumococcal serotypes have been developed and one of them, that including the greatest number of serotypes (PCV13), has been licensed for the use  ...  This web-application is protected by an authentication system, a relief tool articulated in multilevel access profile for data legal protection and patients' privacy.  ... 
doi:10.1186/1824-7288-40-s1-a22 pmcid:PMC4132545 fatcat:zqwmnovq55fcjgfrxvul65v5mq

XXIV World Allergy Congress 2015

Heung-Man Lee, Il-Ho Park, Jae-Min Shin, Hyun-Sun Yoon, Gyeong Yul Park, Margit Zeher, Katsuhiko Matsui, Saki Tamai, Reiko Ikeda, Drsushil Suri, Dranu Suri, Marzieh Heidarzadeh Arani (+3560 others)
2016 The World Allergy Organization Journal  
For providing allergen extracts which were used for NPT, we also appreciate Research Center for Standardization of Allergic Diseases (RCSAD) of Yonsei University supported by a grant from the Korea Healthcare  ...  We thank to ThermoFisher Scientific Korea for support in measuring serum total and allergenspecific IgE/IgG 4 (ImmunoCAP®).  ...  Retrospectively with the medical chart review we investigated the incidence of side reaction of SCIT, relationship between the doses, concentration of allergen.  ... 
doi:10.1186/s40413-016-0096-1 fatcat:k2f4tpykangjzlbkzfpiliyzm4

Late Breaking Poster Session LB TPS

2017 Allergy. European Journal of Allergy and Clinical Immunology  
Statistical analysis was performed using SPSS software.  ...  The new treatment was accepted by patients, with many children preferring the taste of the new treatment and experiencing minimal side effects.  ...  Big food chain restaurants were not included in this study.  ... 
doi:10.1111/all.13249 fatcat:kjxhdffwuva3tgvl4qjeced64u

Risks from Low Doses of Radiation: Continued

M. Goldman
1996 Science  
Astronomy, Chemistry and Biochemistry Departments of UCLA in collaboration with the Jules Stein Eye Institute of the UCLA Medical School, which has active biophysics-related research programs that include protein-folding  ...  Exceptionally well-qualified junior applicants will also be considered for appointment at the assistant or associate professor level.  ...  Research will focus on the development of novel algorithms and software tools for the analysis of molecular sequence data and for the automation of primary and tertiary structures.  ... 
doi:10.1126/science.273.5275.561d fatcat:judbhnacbjgknmogqkklrjfo5y

EAACI Molecular Allergology User's Guide

P. M. Matricardi, J. Kleine-Tebbe, H. J. Hoffmann, R. Valenta, C. Hilger, S. Hofmaier, R. C. Aalberse, I. Agache, R. Asero, B. Ballmer-Weber, D. Barber, K. Beyer (+53 others)
2016 Pediatric Allergy and Immunology  
This information provides the basis for a refined , earlier , diagnosis of the allergic reactions and ultimately for a tailored individualized management of the patient, including opportunities for prevention  ...  This User's Guide for Molecular Allergology will be another breakthrough in this regard.  ...  We would like to thank Araceli Dıaz-Perales, from ETSIA UPM, Madrid, for providing the figure on melon profilin in Section C01, as well as Figure 1 in Section C03.  ... 
doi:10.1111/pai.12563 pmid:27288833 fatcat:u64c6gm5enhj7h6g4r5xddnk6u
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