J. Comput. Biol. - Statistical significance of threading scores.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ model(3404) distribut(989) bayesian(671) }
{ group(2977) signific(1463) compar(1072) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(984) reconstruct(947) comput(926) }
{ studi(1119) effect(1106) posit(819) }
{ measur(2081) correl(1212) valu(896) }
{ concept(1167) ontolog(924) domain(897) }
{ model(2220) cell(1177) simul(1124) }
{ model(3480) simul(1196) paramet(876) }
{ intervent(3218) particip(2042) group(1664) }
{ estim(2440) model(1874) function(577) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ assess(1506) score(1403) qualiti(1306) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ case(1353) use(1143) diagnosi(1136) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ age(1611) year(1155) adult(843) }
{ sampl(1606) size(1419) use(1276) }
{ structur(1116) can(940) graph(676) }
{ activ(1452) weight(1219) physic(1104) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

We present a general method for assessing threading score significance. The threading score of a protein sequence, thread onto a given structure, should be compared with the threading score distribution of a random amino-acid sequence, of the same length, thread on the same structure; small p-values point significantly high scores. We claim that, due to general protein contact map properties, this reference distribution is a Weibull extreme value distribution whose parameters depend on the threading method, the structure, the length of the query and the random sequence simulation model used. These parameters can be estimated off-line with simulated sequence samples, for different sequence lengths. They can further be interpolated at the exact length of a query, enabling the quick computation of the p-value.

Resumo Limpo

present general method assess thread score signific thread score protein sequenc thread onto given structur compar thread score distribut random aminoacid sequenc length thread structur small pvalu point signific high score claim due general protein contact map properti refer distribut weibul extrem valu distribut whose paramet depend thread method structur length queri random sequenc simul model use paramet can estim offlin simul sequenc sampl differ sequenc length can interpol exact length queri enabl quick comput pvalu

Resumos Similares

Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,85495311641543 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,851202636458331 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,848692948173673 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,836577135561808 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,829210498131925 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,820421446816925 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,81685682651372 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,81560072831817 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,81414457013768 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,814109869795382 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,812150192911175 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,811001790489072 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,809650782889704 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,808192753753797 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,807468620249373 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,80282645055875 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,80258389902826 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,80156999400862 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,793404834892824 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,793111418706385 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,790827398083287 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,78902604701372 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,782573523535012 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,782158452399636 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,780308999654111 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,779432617973104 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,775624286633102 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,774435711047163 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,773665951743815 )
Comput Biol Chem - Investigating long range correlation in DNA sequences using significance tests of conditional mutual information. ( 0,770950226683551 )
J. Comput. Biol. - Statistical significance of normalized global alignment. ( 0,770770179018101 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,77028987644565 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,76836803525746 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,768179253561516 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,76617845595189 )
Comput Biol Chem - Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes. ( 0,760567817835144 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,760521461912916 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,760476407697573 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,759526467633482 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,75934755895151 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,758855330432735 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,756607248640984 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,75431540321085 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,754028806748643 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,751342555063576 )
J Biomed Inform - A kinetic model-based algorithm to classify NGS short reads by their allele origin. ( 0,75 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,746315332147772 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,745707135748977 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,74560704311221 )
Med Biol Eng Comput - The influence of alignment-free sequence representations on the semi-supervised classification of class C G protein-coupled receptors: semi-supervised classification of class C GPCRs. ( 0,744234779027762 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,742559357820932 )
J Chem Inf Model - Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. ( 0,740819534906166 )
Comput Biol Chem - Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. ( 0,740033732098322 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,739292968512632 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,73851928059534 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,737859164324666 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,736351397666392 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,735158411688155 )
J. Comput. Biol. - Accurate estimations of evolutionary times in the context of strong CpG hypermutability. ( 0,73461154783572 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,733848964862254 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,732819113627052 )
J. Comput. Biol. - The distribution of word matches between Markovian sequences with periodic boundary conditions. ( 0,732503259606372 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,732266653216813 )
Comput Methods Programs Biomed - Can computational biology improve the phylogenetic analysis of insulin? ( 0,731209957468449 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,731134681518129 )
Comput Biol Chem - Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures. ( 0,725706319844672 )
Med Biol Eng Comput - Characterization and prediction of mRNA polyadenylation sites in human genes. ( 0,72477191782469 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,724236513616185 )
J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model. ( 0,724068136964825 )
Comput. Biol. Med. - New layers in understanding and predicting a-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. ( 0,722470396223807 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,721974964991016 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,721095370560593 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,720897671636306 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,719333729292869 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,718687838684762 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,715831417187356 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,714151339648908 )
Comput Math Methods Med - ADLD: a novel graphical representation of protein sequences and its application. ( 0,714009713204353 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,712952785537385 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,711460354503471 )
Brief. Bioinformatics - Identify drug repurposing candidates by mining the protein data bank. ( 0,709676529623905 )
J. Comput. Biol. - A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. ( 0,70811540418357 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,707845855401651 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,706816990706336 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,706763442112562 )
J. Comput. Biol. - LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value. ( 0,706745174723857 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,706697015714978 )
Comput. Biol. Med. - Gene comparison based on the repetition of single-nucleotide structure patterns. ( 0,706570534673041 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,703667955110233 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,700643035023974 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,700148587360427 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,692012968930687 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,69111496101681 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,690663785792387 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,689307096439987 )
J. Comput. Biol. - A probabilistic model for sequence alignment with context-sensitive indels. ( 0,688302244635678 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,688186230132376 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,684976072904684 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,683027897933489 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,682441172824799 )