Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 48 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 25563 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 51 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 47 site 9 SARS 7 RNA 5 protein 4 virus 4 cleavage 4 Fig 3 specie 3 selection 3 RBD 3 CoV-2 2 study 2 structure 2 sequence 2 result 2 peptide 2 method 2 laboratory 2 function 2 figure 2 enzyme 2 dna 2 cell 2 activity 2 University 2 PCR 2 MERS 1 viral 1 trial 1 tourism 1 substrate 1 station 1 spacer 1 sialic 1 service 1 serine 1 role 1 residue 1 resident 1 proteolytic 1 protease 1 process 1 plot 1 perch 1 patient 1 pathogen 1 nedd4 1 molecular 1 membrane 1 local Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 4150 site 4060 protein 1449 structure 1127 sequence 1103 cell 1012 study 938 virus 812 analysis 801 interaction 793 acid 769 domain 761 method 758 residue 753 cleavage 700 result 698 % 627 activity 625 enzyme 606 specie 604 datum 581 tourism 562 function 560 model 549 region 529 protease 498 peptide 493 system 482 binding 471 inhibitor 462 type 455 gene 440 effect 436 level 434 substrate 433 amino 409 number 408 change 398 process 397 time 397 group 396 role 383 receptor 380 surface 378 factor 375 selection 374 target 368 complex 362 rate 357 ligand 356 host Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 830 al 681 et 618 . 465 SARS 448 RNA 328 Fig 283 C 254 CoV-2 196 CoV 193 A 182 SOX 179 University 154 S 152 Table 136 N 134 MERS 126 ACE2 118 NMR 104 M 99 mRNA 99 MDI 98 T 96 E. 91 tRNA 90 II 89 de 89 RBD 89 MD 88 Protein 88 Aruba 85 pH 83 K 82 GFP 82 D 79 PCR 77 PDB 76 HCV 76 ET 75 FRAD 73 m 73 Institute 70 Department 70 B 68 COVID-19 65 NA 64 Research 61 MS 57 mg 55 HIV-1 55 Caribbean Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2236 we 928 it 358 they 163 them 142 i 73 us 27 itself 24 themselves 8 you 8 one 7 he 3 mrnas 2 ppifs 2 ourselves 2 cb562 1 yegfp 1 theirs 1 t 1 p110a 1 ours 1 nsp7 1 nsp10 1 mg 1 me 1 j?fl«u 1 iv-3l3r. 1 imagej 1 grch37 1 fbp17 1 cys122ser 1 az1c 1 asap2 1 a1-antitrypsin Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 14056 be 2387 have 1899 use 1170 bind 968 show 669 identify 665 base 592 find 475 include 458 suggest 422 provide 412 predict 380 do 363 contain 351 determine 335 indicate 332 increase 316 know 314 involve 310 compare 298 observe 292 detect 289 reveal 277 form 263 make 263 develop 259 perform 257 result 253 occur 248 describe 247 express 245 follow 245 associate 238 require 234 allow 231 obtain 228 induce 224 study 220 investigate 219 demonstrate 213 consider 212 see 206 relate 205 report 205 generate 205 analyze 204 present 203 represent 202 cause 200 lead Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1022 not 847 also 788 high 734 - 634 other 627 more 615 different 600 structural 567 human 522 specific 507 such 491 well 476 viral 472 most 444 molecular 431 new 418 only 393 however 384 functional 383 large 368 small 359 important 355 low 348 active 329 first 315 non 312 thus 298 several 293 similar 275 many 271 positive 261 as 255 like 255 highly 255 further 242 single 240 present 229 local 228 potential 227 then 226 here 220 secondary 211 proteolytic 211 catalytic 210 multiple 209 same 207 significant 199 therefore 186 very 186 common Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 152 most 75 high 74 least 68 good 40 Most 29 large 21 close 20 low 15 short 14 great 11 small 9 near 8 late 6 bad 5 strong 4 fast 3 steep 3 postt 2 old 2 long 2 hard 2 big 2 -which 1 wide 1 topmost 1 slow 1 slim 1 simple 1 preS1 1 northernmost 1 lowermost 1 furth 1 few 1 easy 1 early 1 dry 1 deep 1 cord-009716-oxahu8nz 1 ScYLV 1 HCO3- 1 4xpnd93d 1 -β Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 320 most 55 least 13 well 1 worst 1 smallest 1 highest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 5 doi.org 3 www 3 creativecommons.org 3 covidclinical.net 2 zinc.docking.org 2 www.nature.com 2 www.cbs.dtu.dk 2 mol.ax 2 hcv.lanl.gov 2 github.com 2 dx.doi.org 2 covidclinical 1 www.weather.gov.sg 1 www.singstat.gov.sg 1 www.mbe 1 www.ictvonline 1 www.hiv.lanl.gov 1 www.cbs 1 weblogo.berkeley.edu 1 vega.github.io 1 sourceforge.net 1 sbi.imim.es 1 ribosome.fandm.edu 1 recode.genetics 1 multalin.toulouse.inra.fr 1 msbiodata.innomol.eu 1 jupyter.org 1 jekyllrb.com 1 ircc.fiu.edu 1 glyconnect.expasy.org 1 evolve 1 euhcvdb.ibcp 1 espript.ibcp.fr 1 data 1 creativecommons 1 covidibd.org 1 cov.lichtargelab.org 1 ccc19.org 1 biocomp.chem.uw.edu.pl 1 altair-viz.github.io 1 abacus.gene.ucl.ac.uk Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://www 3 http://covidclinical.net 2 http://zinc.docking.org/substances/subsets/fda/ 2 http://covidclinical 1 http://www.weather.gov.sg/climate-historical-daily/ 1 http://www.singstat.gov.sg/statistics/browse-by-theme/ 1 http://www.nature.com/reprintsPublisher's 1 http://www.nature.com/ 1 http://www.mbe 1 http://www.ictvonline 1 http://www.hiv.lanl.gov 1 http://www.cbs.dtu.dk/services/ 1 http://www.cbs.dtu.dk 1 http://www.cbs 1 http://weblogo.berkeley.edu 1 http://vega.github.io 1 http://sourceforge.net/projects/ADSETMEAS/along 1 http://sbi.imim.es/archer 1 http://ribosome.fandm.edu 1 http://recode.genetics 1 http://multalin.toulouse.inra.fr/multalin/ 1 http://msbiodata.innomol.eu 1 http://mol.ax/delta 1 http://mol.ax/3seq 1 http://jupyter.org 1 http://jekyllrb.com/ 1 http://ircc.fiu.edu 1 http://hcv.lanl.gov/content/immuno/immuno-main.htm 1 http://hcv.lanl.gov/content/hcv-db/Distances/HCV_vari 1 http://glyconnect.expasy.org 1 http://github.com/cgseitz 1 http://github.com/ 1 http://evolve 1 http://euhcvdb.ibcp 1 http://espript.ibcp.fr/ESPript/ESPript/ 1 http://dx.doi.org/10.1016/j.virusres.2015.05 1 http://dx.doi.org/10.1016/j.bios.2012.09.066 1 http://doi.org/10.1038/s42003-020-01370-w.Correspondence 1 http://doi.org/10.1038/ 1 http://doi.org/10.1016/j.watres.2018.03.017 1 http://doi.org/10.1016/j.antiviral.2020.104742 1 http://doi.org/10.1007/s41324-020-00330-0 1 http://data 1 http://creativecommons.org/licenses/by-nc/4.0/ 1 http://creativecommons.org/licenses/ 1 http://creativecommons.org/ 1 http://creativecommons 1 http://covidibd.org 1 http://cov.lichtargelab.org 1 http://ccc19.org Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 zoltan.kapui@sanofi-aventis.com 1 yurst@inr.liu.se 1 yossef.kliger@gmail.com 1 yoshiyuki-tamada@senju.co.jp 1 tompa@enzim.hu 1 tcherno@emory.edu 1 tavernarakis@imbb.forth.gr 1 saleh38@hotmail.com 1 rebecca.lew@med.monash.edu.au 1 noelene.quinsey@med.monash.edu.au 1 myyoon@hanyang.ac.kr 1 michael.teufel@sanofi-synthelabo.com 1 mhoward@genetics.utah.edu 1 maurice.petitou@sanofi-aventis.com 1 lulla@ut.ee 1 lmurillo@univ-lr.fr 1 krishna.bhattiprolu@uni-graz.at 1 kliger@compugen.co.il 1 kay.hofmann@memorec.com 1 july@ludens.elte.hupr 1 journals.permissions@oup.com 1 joheuvel@zedat.fu-berlin.de 1 huber@biochem.mpg.de 1 grzyw@hermes.umcs.lublin.pl 1 gozde_baydar@hotmail.com 1 gl@ludens.elte.hu 1 gal@enzim.hu 1 eva.x.janas@gsk.com 1 eruback@biof.ufrj.br 1 doege@physio.uni-luebeck.de 1 dennis.daniel@childrens.harvard.edu 1 craik@cgl.ucsf.edu 1 colin.gordon@hgu.mrc.ac.uk 1 cnatha@lsuhsc.edu 1 alkova@cerberus.elte.hu 1 albecka@mail.biu.ac.il 1 adam.clauss@klkemi.mas.lu.se 1 mara.kozic@liverpool.ac.uk 1 4ce@i2b2foundation.org Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 9 acid binding sites 8 data are available 5 protein is not 5 sites are not 4 domains do not 4 sites are also 3 activity is also 3 cleavage is not 3 data were not 3 function is still 3 site does not 3 site is not 3 sites are currently 3 sites are highly 3 sites are often 3 sites were also 3 species detected most 2 % were absent 2 acid binding domain 2 acids are favorable 2 acids are often 2 acids were reverse 2 activity does not 2 data are consistent 2 data were unavailable 2 enzyme is not 2 enzymes have very 2 function using local 2 interactions are not 2 method has also 2 method is also 2 methods compare synonymous 2 model was further 2 peptides are also 2 protein binding affinity 2 protein does not 2 protein is also 2 protein is essential 2 protein is present 2 protein is responsible 2 proteins are covalently 2 proteins is crucial 2 proteins is important 2 regions are potentially 2 residues based solely 2 results are also 2 results are consistent 2 results shown here 2 results were similar 2 results were then Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 activity has no effect 1 analysis found no significant 1 cleavage was no more 1 data revealed no significance 1 data showed no evidence 1 data were not available 1 data were not multivariate 1 data were not reliable 1 domain was not part 1 domains do not appreciably 1 enzyme is not able 1 enzyme is not only 1 function is not completely 1 interactions are not due 1 method is not fit 1 model is not compatible 1 peptide showing no significant 1 peptide was not any 1 protein are not equally 1 protein is not catalytically 1 protein is not solely 1 proteins are not limited 1 region is not well 1 residue is not methionine 1 residues are not only 1 residues did not completely 1 sequence does not significantly 1 sequences are not similar 1 site is no longer 1 site is not polymorphic 1 site was not independent 1 sites are not adequately 1 sites are not necessarily 1 sites are not proteolytic 1 sites contained no strong 1 sites had not yet 1 sites is not as 1 sites reveal no obvious 1 sites were not entirely 1 species are not necessarily 1 species do not equally 1 structures is not accurate 1 studies is not possible 1 studies were no longer 1 tourism has no significant 1 viruses did not severely A rudimentary bibliography -------------------------- id = cord-356264-q0yqnlyl author = Armijos-Jaramillo, Vinicio title = SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-03-23 keywords = RBD; SARS; selection; site summary = doi = 10.1101/2020.03.21.001933 id = cord-260657-yf8fvx7k author = Bekaert, Michaël title = An Extended Signal Involved in Eukaryotic −1 Frameshifting Operates through Modification of the E Site tRNA date = 2005-01-07 keywords = site summary = doi = 10.1016/j.molcel.2004.12.009 id = cord-276405-yfvu83r9 author = Brat, Gabriel A. title = International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium date = 2020-08-19 keywords = COVID-19; datum; laboratory; patient; site summary = doi = 10.1038/s41746-020-00308-0 id = cord-300117-rlpzejjt author = Coutard, B. title = The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade date = 2020-02-10 keywords = SARS; site summary = doi = 10.1016/j.antiviral.2020.104742 id = cord-013443-x74uxdi4 author = Daniel, Dennis A. title = Pediatric Resident Engagement With an Online Critical Care Curriculum During the Intensive Care Rotation* date = 2020-06-25 keywords = ICU; resident; site summary = doi = 10.1097/pcc.0000000000002477 id = cord-271514-sls3bsm0 author = Dean, Natalie E. title = Ensemble Forecast Modeling for the Design of COVID-19 Vaccine Efficacy Trials date = 2020-09-15 keywords = site; trial summary = doi = 10.1016/j.vaccine.2020.09.031 id = cord-327069-vjlisnui author = Driscoll, Amanda J. title = Standardization of Laboratory Methods for the PERCH Study date = 2017-06-15 keywords = PCR; laboratory; perch; site summary = doi = 10.1093/cid/cix081 id = cord-275307-d7htyfcl author = Gaglia, Marta Maria title = Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date = 2015-12-08 keywords = Fig; GFP; RNA; SOX; cut; site summary = Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5'' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . doi = 10.1371/journal.ppat.1005305 id = cord-267326-355q6k6k author = Gu, Xiaoqiong title = Geospatial distribution of viromes in tropical freshwater ecosystems date = 2018-06-15 keywords = RNA; Singapore; site; viral; virus summary = This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. doi = 10.1016/j.watres.2018.03.017 id = cord-262318-qpztmdnw author = Guo, Jingxu title = In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors date = 2020-07-16 keywords = Fig; RNA; SV3CP; site summary = doi = 10.1016/j.yjsbx.2020.100031 id = cord-009730-lc8712xm author = HODKINSON, I. D. title = The distribution, abundance and host plant relationships of Salix‐ feeding psyllids (Homoptera: Psylloidea) in arctic Alaska date = 2008-03-14 keywords = Hodkinson; Salix; Site; catkin summary = doi = 10.1111/j.1365-2311.1979.tb00568.x id = cord-048327-xgwbl8em author = Henderson, Clark M. title = Antisense-induced ribosomal frameshifting date = 2006-08-18 keywords = RNA; UGA; site summary = doi = 10.1093/nar/gkl531 id = cord-259195-bmz8995u author = Huang, Chih-Cheng title = AlGaN/GaN high electron mobility transistors for protein–peptide binding affinity study date = 2013-03-15 keywords = site summary = doi = 10.1016/j.bios.2012.09.066 id = cord-341968-uc8i9h0m author = Izaguirre, Gonzalo title = The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date = 2019-09-09 keywords = cleavage; furin; site; virus summary = doi = 10.3390/v11090837 id = cord-315951-5gsbtfag author = Kiemer, Lars title = Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date = 2004-06-06 keywords = SARS; cleavage; site summary = doi = 10.1186/1471-2105-5-72 id = cord-007199-ol2du7ph author = Kliger, Yossef title = Predicting proteolytic sites in extracellular proteins: only halfway there date = 2008-04-15 keywords = Swiss; proteolytic; site summary = doi = 10.1093/bioinformatics/btn084 id = cord-028681-e2zh6092 author = Koide, Takashi title = It Never Rains but It Pours: Analyzing and Detecting Fake Removal Information Advertisement Sites date = 2020-06-11 keywords = frad; site summary = doi = 10.1007/978-3-030-52683-2_9 id = cord-321150-ev6acl7b author = Lam, Ha Minh title = Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm date = 2017-10-03 keywords = sequence; site summary = doi = 10.1093/molbev/msx263 id = cord-263033-4790dhc5 author = Laptev, I. G. title = Posttranscriptional modification of messenger RNAs in eukaryotes date = 2015-12-11 keywords = FTO; RNA; site summary = doi = 10.1134/s002689331506014x id = cord-274409-4ugdxbmy author = Laskar, Rezwanuzzaman title = Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date = 2020-10-19 keywords = Disease; SARS; site summary = title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India Further, constitution of ''Disease'' mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. With a definitive possibility of India becoming the most affected country by SARS-CoV-2 in near future and the demographic burden involved, its pertinent to be analyze the accumulating variations in the genome accounting for possible changes in protein and their potential to alter the virus in any manner. Herein we extend our study using the same congregation of sequences to analyze the nature and composition of the observed mutations and their impact on proteins of SARS-CoV-2. The distribution of Disease and Neutral variants across the different genes of SARS-CoV-2 has been shown in Table 4 and Supplementary file 5. doi = 10.1101/2020.10.19.345066 id = cord-009716-oxahu8nz author = Lawes, Roger A. title = Comparing agglomerative clustering and three weed classification frameworks to assess the invasiveness of alien species across spatial scales date = 2006-10-27 keywords = cover; site; specie summary = doi = 10.1111/j.1472-4642.2006.00291.x id = cord-346965-0oq2n0af author = Liu, Zhi-Ping title = Bridging protein local structures and protein functions date = 2008-04-18 keywords = dna; function; local; method; protein; site; structure summary = The characteristics between interface and noninterface portions of a protein surface, such as sequence conservation, proportions of amino acids, secondary structure, solvent accessibility and side-chain conformational entropy, are often used to distinguish the specificity of local structures relating to protein binding function. The method relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologs. (2006) improved previous approaches by combining two known measures of ''functionality'' in proteins, i.e. cleft volume and residue conservation, to develop a method for identifying the location of ligand-binding pockets in proteins. (2006) applied an SVM method to predict DNA-binding sites using the features including amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. (2006) developed a method to predict both protein-protein binding site location and interface type (obligate or non-obligate) using a Bayesian network in combination with surface patch analysis. doi = 10.1007/s00726-008-0088-8 id = cord-024166-t3qxscbp author = Losvik, Mary H. title = Plant species diversity in an old, traditionally managed hay meadow compared to abandoned hay meadows in southwest Norway date = 2008-06-28 keywords = Losvik; plot; site; specie summary = doi = 10.1111/j.1756-1051.1999.tb01231.x id = cord-010307-sxh5mq1q author = MILNE, D. J. title = Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas date = 2005-11-23 keywords = Australia; bat; end; site; specie summary = doi = 10.1111/j.1442-9993.2005.01535.x id = cord-322129-uyswj4ow author = Melin, Amanda D. title = Comparative ACE2 variation and primate COVID-19 risk date = 2020-10-27 keywords = ACE2; CoV-2; SARS; Supplementary; site summary = doi = 10.1038/s42003-020-01370-w id = cord-018103-czjjnlkf author = Moon, Sanghoon title = Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome date = 2006 keywords = frameshift; site summary = We have developed a web-based application program called FSFinder2 for predicting frameshift sites of general type. In previous work we developed a program called FSFinder (Frameshift Signal Finder) for predicting -1 and +1 frameshift sites [5] . In previous experimental results of testing FSFinder2 on ~190 genomic and partial DNA sequences showed that it predicted frameshift sites efficiently and with greater sensitivity and specificity than other programs, because it focused on the overlapping regions of ORFs and prioritized candidate signals (For -1 frameshifts, sensitivity was 0.88 and specificity 0.97; for +1 frameshifts, sensitivity was 0.91 and specificity 0.94) [5] [6] [7] . coli K12 genome sequence, we found 18,401 frameshift sites after the X XXY YYZ motif. Among these sequences, 11,530 frameshift sites included secondary structure such as pseudoknots or stem-loops. Among these sites, 11 sites including 3 known frameshift sites were considered significant based on the gene length, shape and the length of overlapping region. doi = 10.1007/11816102_65 id = cord-332948-h297ukuu author = Olotu, Fisayo A. title = Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date = 2020-10-16 keywords = CoV-2; RBD; SARS; protein; site summary = doi = 10.1016/j.imu.2020.100451 id = cord-332855-u0amf1oh author = Parsons, Lisa M. title = Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding date = 2019-03-22 keywords = Fig; M41; RBD; site summary = doi = 10.1074/jbc.ra119.007532 id = cord-024619-0wihqs9i author = Parvin, Farhana title = Accessibility and site suitability for healthcare services using GIS-based hybrid decision-making approach: a study in Murshidabad, India date = 2020-05-11 keywords = GIS; accessibility; healthcare; service; site summary = doi = 10.1007/s41324-020-00330-0 id = cord-034684-ehaiqye5 author = Peterson, Ryan R. title = Over the Caribbean Top: Community Well-Being and Over-Tourism in Small Island Tourism Economies date = 2020-11-05 keywords = Aruba; CBS; Caribbean; Duval; Peterson; community; site; tourism summary = doi = 10.1007/s42413-020-00094-3 id = cord-304421-xpj6c0vx author = Piñón, Josefina D. title = Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b date = 1999-10-25 keywords = A59; MHV; cleavage; site summary = doi = 10.1006/viro.1999.9954 id = cord-338980-pygykil7 author = Rahaman, Jordon title = Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date = 2016-11-09 keywords = MERS; SARS; protein; site summary = doi = 10.1093/gbe/evw246 id = cord-000294-2g471tb4 author = Rhodin, Michael H. J. title = A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding date = 2010-08-12 keywords = L11; PRF; site summary = doi = 10.1093/nar/gkq711 id = cord-332165-31tbc31x author = Rustmeier, Nils H. title = The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date = 2019-10-14 keywords = acid; figure; sialic; site; virus summary = doi = 10.3390/v11100947 id = cord-336034-13u8njtt author = Scott, Shannon D title = Barriers and supports to implementation of MDI/spacer use in nine Canadian pediatric emergency departments: a qualitative study date = 2009-10-13 keywords = MDI; site; spacer summary = doi = 10.1186/1748-5908-4-65 id = cord-103085-vf4qyvft author = Seitz, Christian title = Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase date = 2020-11-02 keywords = Influenza; figure; glycan; site summary = Using Brownian dynamics simulations, we observe a twoto eight-fold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. We have utilized BD to estimate the rates of binding of small molecules to the primary (i.e. active/catalytic) and secondary (i.e. hemadsorption) binding sites of influenza neuraminidase in glycosylated and unglycosylated states. The protein-ligand atom pairs were taken from crystal structures of ligands in the primary and secondary sites of neuraminidase for each monomer, and simulations were run for the full tetramer. Keeping in mind the primary and secondary binding sites are located just beneath the glycans (Figure 1) , the size and flexibility of the glycans here shows that they have the capability to "shield" the binding sites from ligand association. (A) The glycan structures from the MD simulations show a moderate association rate inhibition to the primary binding site irrespective of ligand chosen. doi = 10.1101/2020.08.12.248690 id = cord-289443-46w52de3 author = Sironi, Manuela title = Evolutionary insights into host–pathogen interactions from mammalian sequence data date = 2015-03-18 keywords = HIV-1; NPC1; host; pathogen; selection; site summary = doi = 10.1038/nrg3905 id = cord-285910-rw2byz31 author = Stahl, Guillaume title = Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding date = 2002-04-01 keywords = codon; site summary = doi = 10.1016/s0968-0004(02)02064-9 id = cord-346532-4xpnd93d author = Strömich, Léonie title = Allosteric Hotspots in the Main Protease of SARS-CoV-2 date = 2020-11-06 keywords = SARS; site summary = doi = 10.1101/2020.11.06.369439 id = cord-314166-79323mzd author = Vanderford, Thomas H. title = Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date = 2006-12-11 keywords = site; virus summary = doi = 10.1093/molbev/msl194 id = cord-010628-71rkpco4 author = WISE, E. J. title = Studies on the Ephemeroptera of a Northumbrian river system: I. Serial distribution and relative abundance date = 2006-05-29 keywords = Coquet; Ephemeroptera; River; site; station summary = doi = 10.1111/j.1365-2427.1976.tb01621.x id = cord-351115-dy81dtnk author = Wang, Chen title = Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date = 2020-10-20 keywords = CoV-2; RNA; SARS; site summary = doi = 10.21203/rs.3.rs-95030/v1 id = cord-317061-0bx704ao author = Wu, Andong title = Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date = 2015-10-02 keywords = Fig; MERS; cleavage; site summary = The nsp5 of the newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as 3CLpro and its canonical cleavage sites (between nsps) were predicted based on sequence alignment, but the cleavability of these cleavage sites remains to be experimentally confirmed and putative non-canonical cleavage sites (inside one nsp) within the pp1a/1ab awaits further analysis. Some cleavage sites have been identified and confirmed by previous studies, including three cleavage sites of PLpros of human coronavirus 229E (HCoV 229E), mouse hepatitis virus (MHV), SARS-CoV, MERS-CoV and infectious bronchitis virus (IBV), whose cleavages release the first 3 non-structural proteins (Bonilla et al., 1995; Kilianski et al., 2013; Lim and Liu, 1998; Ziebuhr et al., 2007) . In order to set up a more moderate and balanced criteria for protease cleavage site identification, we compared six scanning conditions with different stringency to systematically predict the 3CLpro cleavage sites on pp1a/1ab of five coronaviruses including MERS-CoV. To rapidly evaluate the proteolysis activity of MERS-CoV 3CLpro toward the predicted cleavage sites of different substrates, a sensitive luciferase-based biosensor assay was adopted. doi = 10.1016/j.virusres.2015.05.018 id = cord-328681-jf2mj16z author = Yang, Ziheng title = Statistical methods for detecting molecular adaptation date = 2000-12-01 keywords = selection; site summary = doi = 10.1016/s0169-5347(00)01994-7 id = cord-018865-melttpiq author = Yu, Tian-fei title = Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems date = 2012 keywords = PCR; TGEV; site summary = doi = 10.1007/978-3-642-27537-1_7 id = cord-316968-rowoylge author = Zhang, Wenjuan title = Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes date = 2006 keywords = HCV; site summary = doi = 10.1007/s11434-006-2118-9 id = cord-001835-0s7ok4uw author = nan title = Abstracts of the 29th Annual Symposium of The Protein Society date = 2015-10-01 keywords = ATP; Biology; Ca21; Chemistry; Department; Institute; NADPH; NMR; PDB; RNA; Science; Tau; University; activity; base; bind; binding; cell; change; complex; design; dna; domain; enzyme; form; function; high; interaction; membrane; method; molecular; peptide; process; protein; residue; result; role; sequence; site; structure; study summary = Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. doi = 10.1002/pro.2823 id = cord-022955-vy0qgtll author = nan title = Proteases date = 2005-06-20 keywords = APC; GCPII; Met; University; activity; cell; enzyme; human; inhibitor; nedd4; peptide; protease; protein; result; serine; site; study; substrate summary = In order to understand the molecular basis of the enzyme-substrate binding mechanism, we employ the synthetic peptide and mass spectrometry-based approaches to investigate the significance of selected amino acid residues that are flanking both sides of the SARS-CoV 3CL pro cleavage site. To contribute to the assignment of a physiological role to genomic-derived peptidases and to make them more accessible for the drug discovery process, we have undertaken a program consisting of mRNA expression profiling, full-length recombinant expression in insect cells, purification and determination of the catalytic activity for the human proteolytic enzymes. This comprehensive analysis of the local backbone properties of SGTI in the free and in the complex form made possible to identify conformational similarities and differences responsible for its efficient binding to the enzyme, and provides a good basis for further studying the structural aspects of protease inhibitor specificity. doi = 10.1111/j.1742-4658.2005.4739_4.x