Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ model(2656) set(1616) predict(1553) }
{ assess(1506) score(1403) qualiti(1306) }
{ age(1611) year(1155) adult(843) }
{ design(1359) user(1324) use(1319) }
{ first(2504) two(1366) second(1323) }
{ result(1111) use(1088) new(759) }
{ process(1125) use(805) approach(778) }
{ data(1737) use(1416) pattern(1282) }
{ featur(3375) classif(2383) classifi(1994) }
{ motion(1329) object(1292) video(1091) }
{ case(1353) use(1143) diagnosi(1136) }
{ imag(1947) propos(1133) code(1026) }
{ system(1976) rule(880) can(841) }
{ patient(2315) diseas(1263) diabet(1191) }
{ chang(1828) time(1643) increas(1301) }
{ extract(1171) text(1153) clinic(932) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ research(1085) discuss(1038) issu(1018) }
{ visual(1396) interact(850) tool(830) }
{ studi(1119) effect(1106) posit(819) }
{ signal(2180) analysi(812) frequenc(800) }
{ drug(1928) target(777) effect(648) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ 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) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ 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) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ 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) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ 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) }
{ 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) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ 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) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Several computational methods exist for the identification of transmembrane beta barrel proteins (TMBs) from sequence. Some of these methods also provide the transmembrane (TM) boundaries of the putative TMBs. The aim of this study is to (1) derive the propensities of the TM residues to be exposed to the lipid bilayer and (2) to predict the exposure status (i.e. exposed to the bilayer or hidden in protein structure) of TMB residues. Three novel propensity scales namely, BTMC, BTMI and HTMI were derived for the TMB residues at the hydrophobic core region of the outer membrane (OM), the lipid-water interface regions of the OM, and for the helical membrane proteins (HMPs) residues at the lipid-water interface regions of the inner membrane (IM), respectively. Separate propensity scales were derived for monomeric and functionally oligomeric TMBs. The derived propensities reflect differing physico-chemical properties of the respective membrane bilayer regions and were employed in a computational method for the prediction of the exposure status of TMB residues. Based on the these propensities, the conservation indices and the frequency profile of the residues, the transmembrane residues were classified into buried/exposed with an accuracy of 77.91% and 80.42% for the residues at the membrane core and the interface regions, respectively. The correlation of the derived scales with different physico-chemical properties obtained from the AAIndex database are also discussed. Knowledge about the residue propensities and burial status will be useful in annotating putative TMBs with unknown structure.

Resumo Limpo

sever comput method exist identif transmembran beta barrel protein tmbs sequenc method also provid transmembran tm boundari putat tmbs aim studi deriv propens tm residu expos lipid bilay predict exposur status ie expos bilay hidden protein structur tmb residu three novel propens scale name btmc btmi htmi deriv tmb residu hydrophob core region outer membran om lipidwat interfac region om helic membran protein hmps residu lipidwat interfac region inner membran im respect separ propens scale deriv monomer function oligomer tmbs deriv propens reflect differ physicochem properti respect membran bilay region employ comput method predict exposur status tmb residu base propens conserv indic frequenc profil residu transmembran residu classifi buriedexpos accuraci residu membran core interfac region respect correl deriv scale differ physicochem properti obtain aaindex databas also discuss knowledg residu propens burial status will use annot putat tmbs unknown structur

Resumos Similares

Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,912004078639657 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,911738637149431 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,901857018479119 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,89702951056152 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,89489848333582 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,888806066591136 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,888755482034613 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,883523528446609 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,881484735253313 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,879695532940437 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,878929258846969 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,872520121177229 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,870992190575512 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,867712690060301 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,867578143973344 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,866209416750156 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,85413159709905 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,853607168506876 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,85179994385639 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,848972816444738 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,841517068785865 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,84050478345219 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,840283893105957 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,839463875490078 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,83928525208584 )
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. ( 0,835535456179414 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,833245637398222 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,831838259557022 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,825896359101711 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,82585124551092 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,824886278149 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,824459250008196 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,823341897402709 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,823151343320242 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,821937266372656 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,81845875891784 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,817760352795182 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,817497884571893 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,814769724622239 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,809071538743957 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,805874777830641 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,804461117249892 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,804152135395611 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,803101747417019 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,80258389902826 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,802114981360474 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,802007413964468 )
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. ( 0,800420373209788 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,797316460747894 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,796544616778344 )
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. ( 0,796533730479332 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,795578263458785 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,793249823837905 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,790717296671423 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,790364963256061 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,788473694881108 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,78687359853023 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,784236665669676 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,783005559664755 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,782043115565503 )
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. ( 0,781649810772239 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,78056311726309 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,77874899286431 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,777803551835395 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,776129746071624 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,773631467404092 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,766284323824066 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,765628190639599 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,762840159452906 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,759717747408695 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,759409082939813 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,758161856545648 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,756243860864163 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,755271719681082 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,7542437893323 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,751676030368143 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,750416292485795 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,747306073833892 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,746751582147815 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,744514369061293 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,74345619613227 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,739240665561081 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,734013611848705 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,733603754167914 )
Comput Math Methods Med - ADLD: a novel graphical representation of protein sequences and its application. ( 0,732129253191204 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,732125575389834 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,731488930153666 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,72998090746137 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,728100751984387 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,727352495021155 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,727213189268618 )
Sci Data - A repository of assays to quantify 10,000 human proteins by SWATH-MS. ( 0,725836527050914 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,725506688012718 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,723896374975516 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,723787433437766 )
Sci Data - A draft genome for the African crocodilian trypanosome Trypanosoma grayi. ( 0,718041999542231 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,717673852689277 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,713171845258129 )
Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties. ( 0,7118973471551 )
Comput Biol Chem - Investigating long range correlation in DNA sequences using significance tests of conditional mutual information. ( 0,70874717828447 )