Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ take(945) account(800) differ(722) }
{ featur(3375) classif(2383) classifi(1994) }
{ perform(1367) use(1326) method(1137) }
{ analysi(2126) use(1163) compon(1037) }
{ detect(2391) sensit(1101) algorithm(908) }
{ measur(2081) correl(1212) valu(896) }
{ model(2341) predict(2261) use(1141) }
{ monitor(1329) mobil(1314) devic(1160) }
{ health(1844) social(1437) communiti(874) }
{ activ(1452) weight(1219) physic(1104) }
{ featur(1941) imag(1645) propos(1176) }
{ spatial(1525) area(1432) region(1030) }
{ patient(2315) diseas(1263) diabet(1191) }
{ chang(1828) time(1643) increas(1301) }
{ control(1307) perform(991) simul(935) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ state(1844) use(1261) util(961) }
{ group(2977) signific(1463) compar(1072) }
{ intervent(3218) particip(2042) group(1664) }
{ patient(1821) servic(1111) care(1106) }
{ structur(1116) can(940) graph(676) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ method(1969) cluster(1462) data(1082) }
{ 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) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ case(1353) use(1143) diagnosi(1136) }
{ 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) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ 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) }
{ method(2212) result(1239) propos(1039) }

Resumo

A new method for remote protein homology detection, called support vector machine incorporating the context of physicochemical properties (SVM-CP), is presented. Recent discriminative methods are based on concatenating information extracted from each protein by considering several physicochemical properties. We show that there are physicochemical properties that reflect the functional or structural characteristics of each specific protein family, but there are also some physicochemical properties that affect the accuracy of the classification techniques. The research highlights the importance of the selection of physicochemical properties in remote homology detection. Most of the methods slide a window over every protein sequence to extract physicochemical information. This extraction is usually performed by giving the same importance to every value in the window, i.e., averaging the physicochemical values in the observation window. SVM-CP takes into account that every residue in a sliding window has a different weight, which reflects the importance or contribution to the representative value of the window. The SVM-CP method reaches a receiver operating characteristic (ROC) score of 0.93462, which is the highest value for a remote homology detection method based on the sequence composition information.

Resumo Limpo

new method remot protein homolog detect call support vector machin incorpor context physicochem properti svmcp present recent discrimin method base concaten inform extract protein consid sever physicochem properti show physicochem properti reflect function structur characterist specif protein famili also physicochem properti affect accuraci classif techniqu research highlight import select physicochem properti remot homolog detect method slide window everi protein sequenc extract physicochem inform extract usual perform give import everi valu window ie averag physicochem valu observ window svmcp take account everi residu slide window differ weight reflect import contribut repres valu window svmcp method reach receiv oper characterist roc score highest valu remot homolog detect method base sequenc composit inform

Resumos Similares

Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,831378345528737 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,796181596765207 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,782859728528121 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,777411673079391 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,753419798273827 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,751203313012201 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,750744249881023 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,748972093560356 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,746385445116375 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,736144310691705 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,735483141715136 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,734862221978544 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,731986533883004 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,728977257449206 )
Comput Biol Chem - Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier. ( 0,728447322632597 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,723331266447237 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,719977093638304 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,719427535295326 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,719349452808778 )
J Chem Inf Model - Proteins as sponges: a statistical journey along protein structure organization principles. ( 0,717370450635201 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,716277784804742 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,715148110462334 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,713725744616633 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,712793637440269 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,712512406030661 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,7118973471551 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,710762778486272 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,70934986437554 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,70899725419371 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,708430926916008 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,707294816499321 )
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. ( 0,706139403219878 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,705449208801306 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,70506372515356 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,702863728069155 )
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. ( 0,702456777489261 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,701590290467295 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,700390516266448 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,698865166297019 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,697218794228531 )
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. ( 0,697051120368541 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,697021472006047 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,694795383963925 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,694393675673322 )
Comput Biol Chem - Practical halving; the Nelumbo nucifera evidence on early eudicot evolution. ( 0,694372274463139 )
Comput Biol Chem - Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza. ( 0,693920436887971 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,687435128530479 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers I: proteins. ( 0,686577979213993 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,685667381988595 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,684583092237184 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,684147247663816 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,684059230550617 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,679575840843478 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,679128401146928 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,675525401945805 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,673735927538912 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,673587650872952 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,671727030517782 )
Comput. Biol. Med. - Remote protein homology detection and fold recognition using two-layer support vector machine classifiers. ( 0,671082992452923 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,669164591503693 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,667547491657059 )
J. Comput. Biol. - Tracing the most parsimonious indel history. ( 0,667009586652833 )
Comput Biol Chem - A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM. ( 0,666117961548022 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,666112469748951 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,664804484620308 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,663400986203519 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,662995434877776 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,660124046802695 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,65753407310486 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,65588118526808 )
Comput Methods Programs Biomed - Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. ( 0,65399364161705 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,652476043583428 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,651212544890976 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,651155729409874 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,646964704118333 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,646583201219264 )
Sci Data - A repository of assays to quantify 10,000 human proteins by SWATH-MS. ( 0,64551168103075 )
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. ( 0,643948177849707 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,643667226161436 )
Brief. Bioinformatics - DRISEE overestimates errors in metagenomic sequencing data. ( 0,643494256022465 )
Comput Biol Chem - PPM-Dom: a novel method for domain position prediction. ( 0,643274750595673 )
J. Comput. Biol. - An automaton approach for waiting times in DNA evolution. ( 0,642725642184102 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,642190463100039 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,641580364938106 )
Curr Protoc Bioinformatics - Clustal omega. ( 0,640298873223498 )
J. Comput. Biol. - Statistical significance of normalized global alignment. ( 0,639610460469848 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,638895189204375 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,638525114043413 )
Comput. Biol. Med. - LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors. ( 0,636870545087194 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,635430562889089 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,635242564585279 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,634650701098505 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,634209239027858 )
Healthc (Amst) - What can the past of pay-for-performance tell us about the future of Value-Based Purchasing in Medicare? ( 0,634071821119079 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,634068836572209 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,63406549301525 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,634051500062847 )
J Integr Bioinform - Predicting genes involved in human cancer using network contextual information. ( 0,633953336240698 )
Comput Biol Chem - Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction. ( 0,633719423583813 )
Brief. Bioinformatics - Computational challenges of sequence classification in microbiomic data. ( 0,632725279034066 )