Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ network(2748) neural(1063) input(814) }
{ featur(3375) classif(2383) classifi(1994) }
{ model(2656) set(1616) predict(1553) }
{ health(1844) social(1437) communiti(874) }
{ measur(2081) correl(1212) valu(896) }
{ learn(2355) train(1041) set(1003) }
{ structur(1116) can(940) graph(676) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ model(2220) cell(1177) simul(1124) }
{ research(1085) discuss(1038) issu(1018) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ medic(1828) order(1363) alert(1069) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ use(976) code(926) identifi(902) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ 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) }
{ imag(2830) propos(1344) filter(1198) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ 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) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ 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) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ 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) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ 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) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q3) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation.

Resumo Limpo

supervis learn recurr neural network wellsuit predict protein secondari structur under amino acid sequenc studi modular reciproc recurr neural network mrrnn propos model strong correl adjac secondari structur element besid multilay bidirect recurr neural network mbrnn introduc captur longrang intramolecular interact amino acid format secondari structur final modular predict system devis base interact integr mrrnn mbrnn structur arbitrarili engag neighbor effect secondari structur type concurr memor sequenti depend amino acid along protein chain advanc combin network augment percentag accuraci q boost segment overlap sov test psipr dataset threefold crossvalid

Resumos Similares

J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,893825434438664 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,840283893105957 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,835777855368652 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,835226072593184 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,829028910773099 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,824924785039533 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,82164509119616 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,82094771040392 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,820819872608766 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,819584558960563 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,813196290413792 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,812968610683109 )
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. ( 0,811245744592635 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,806759265640671 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,80582296402538 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,803550296686671 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,803133529989356 )
J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model. ( 0,798953033998403 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,79732965448557 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,79555930753044 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,79526998635957 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,794665215448968 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,788078021023816 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,786454801810301 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,786255485900996 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,785994301826007 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,78574728389157 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,782609842200917 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,781479477359455 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,778780470906684 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,778570339690313 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,774014921754806 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,773737792943994 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,772332016987598 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,771522971694644 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,770359718791125 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,768428458272008 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,767970781687138 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,767800489067059 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,767246280949697 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,76597786133968 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,765566832969047 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,762533428300349 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,762375576593142 )
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. ( 0,761639123796372 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,760691491170943 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,756821192671213 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,754247233265651 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,753041133055184 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,75285791480042 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,748069456529384 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,745634632059805 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,744774969161662 )
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. ( 0,74257859654841 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,741725149385313 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,741479695661219 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,73573416677347 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,73552843618981 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,735158411688155 )
Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties. ( 0,734862221978544 )
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. ( 0,733367968387835 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,728394199747288 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,728228592465015 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,727097404011756 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,72580419314835 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,725789587664237 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,723448534142252 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,721537531823008 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,720848066070121 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,720354107665991 )
Comput. Biol. Med. - A protein mapping method based on physicochemical properties and dimension reduction. ( 0,720082299823096 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,716699502196614 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,716408606793026 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,71475391544946 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,714673225538863 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,713728910993908 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,712023972325944 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,709320723299229 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,704007705646679 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,702348753404797 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,701615575878308 )
Brief. Bioinformatics - Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks. ( 0,700952558119903 )
IEEE Trans Pattern Anal Mach Intell - Spatiotemporal Alignment of Visual Signals on a Special Manifold. ( 0,699447985537202 )
Comput Biol Chem - Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier. ( 0,699150073214899 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,698549940962132 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,6956663299834 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,694814652080401 )
J. Comput. Biol. - A probabilistic model of neutral and selective dynamics of protein network evolution. ( 0,69377008344649 )
Comput Biol Chem - In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: a growing comparative genomics resource. ( 0,692545078679777 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,692157436949231 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,690793047290546 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,687190011128743 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,686295950881369 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,685465545230853 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,681013582882032 )
J Chem Inf Model - Proteins as sponges: a statistical journey along protein structure organization principles. ( 0,680879026928084 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,679212025832036 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,67850233238228 )
Comput Methods Programs Biomed - Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. ( 0,678113769229846 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,677052482501541 )