Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ bind(1733) structur(1185) ligand(1036) }
{ visual(1396) interact(850) tool(830) }
{ inform(2794) health(2639) internet(1427) }
{ error(1145) method(1030) estim(1020) }
{ clinic(1479) use(1117) guidelin(835) }
{ data(3963) clinic(1234) research(1004) }
{ model(3480) simul(1196) paramet(876) }
{ state(1844) use(1261) util(961) }
{ signal(2180) analysi(812) frequenc(800) }
{ can(981) present(881) function(850) }
{ result(1111) use(1088) new(759) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ imag(1057) registr(996) error(939) }
{ take(945) account(800) differ(722) }
{ framework(1458) process(801) describ(734) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ case(1353) use(1143) diagnosi(1136) }
{ system(1050) medic(1026) inform(1018) }
{ ehr(2073) health(1662) electron(1139) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ gene(2352) biolog(1181) express(1162) }
{ first(2504) two(1366) second(1323) }
{ analysi(2126) use(1163) compon(1037) }
{ drug(1928) target(777) effect(648) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ model(3404) distribut(989) bayesian(671) }
{ data(1737) use(1416) pattern(1282) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ 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) }
{ 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) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ 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) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(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) }
{ studi(1119) effect(1106) posit(819) }
{ 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) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ 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) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved in protein-protein interactions as well as binding to other ligand molecules. The identification of internal sequence repeats in the primary structure is not sufficient for the analysis of structural repeats. Thus, a new method called ProSTRIP has been developed using dynamic programming to find the similar structural repeats in a three-dimensional protein structure. The detection of these repeats is made by calculating the protein backbone Calpha angles. An internet computing server is also created by implementing this method and enables graphical visualization of the results. It can be freely accessed at http://cluster.physics.iisc.ernet.in/prostrip/.

Resumo Limpo

occurr similar structur repeat protein structur evolv gene duplic repeat act structur build block form one compact structur function unit call repeat domain protein famili compris similar structur repeat main involv proteinprotein interact well bind ligand molecul identif intern sequenc repeat primari structur suffici analysi structur repeat thus new method call prostrip develop use dynam program find similar structur repeat threedimension protein structur detect repeat made calcul protein backbon calpha angl internet comput server also creat implement method enabl graphic visual result can freeli access httpclusterphysicsiiscernetinprostrip

Resumos Similares

Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,912212044674341 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,909647643222137 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,908010476907815 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,905481384255664 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,903791577699349 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,901857018479119 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,895792577386384 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,895397326321843 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,888266369755002 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,887595348760422 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,880243385180091 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,879524366031593 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,878787878787879 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,878202433175401 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,876698014629049 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,876696463402523 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,872099844648996 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,866703776533039 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,86307519640853 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,859304050959662 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,858908224767226 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,856623397365935 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,856283746312024 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,85398649245344 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,851450759655062 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,847051381917431 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,844755408904167 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,84268335060627 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,840410163732727 )
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. ( 0,83759314125711 )
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. ( 0,837486481924951 )
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. ( 0,837047970029752 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,833738037965128 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,833461242621475 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,831175070956567 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,827424101237285 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,827390950761629 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,825865147767374 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,824622558536586 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,821429602886928 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,821143354530761 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,820992757862049 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,820198364382594 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,820083023444876 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,819891591749923 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,812150192911175 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,811879378111472 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,810309764192496 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,809946802789938 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,808059959796834 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,805826022751646 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,803133529989356 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,803063425029192 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,801916867519958 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,798491987349053 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,786767399640662 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,784050907514009 )
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. ( 0,782783859627386 )
Comput Math Methods Med - ADLD: a novel graphical representation of protein sequences and its application. ( 0,781444960029314 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,778519237124646 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,773618538324421 )
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. ( 0,773185754149361 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,772857956179213 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,771142108901828 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,768467370284919 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,766453381267259 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,763369725387968 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,760995782623212 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,759761023864173 )
Brief. Bioinformatics - Identify drug repurposing candidates by mining the protein data bank. ( 0,759423813802197 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,759391762796465 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,75854051124636 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,758278033303142 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,758219639794268 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,758047039249712 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,756877315168416 )
Curr Protoc Bioinformatics - Using the structure-function linkage database to characterize functional domains in enzymes. ( 0,756539318160646 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,756187068024453 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,755995122641507 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,755863042864443 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,755544446503036 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,753971130759901 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,753458137254454 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,751307554348112 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,75126835888634 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,750497011309842 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,749676135822782 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,749115690370937 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,748408484168118 )
Comput. Biol. Med. - Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae. ( 0,74703557312253 )
Comput Math Methods Med - Analyzing effects of naturally occurring missense mutations. ( 0,74535599249993 )
J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model. ( 0,74399382487688 )
Brief. Bioinformatics - Genome variation discovery with high-throughput sequencing data. ( 0,742711314761424 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,741740937498691 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,741535207428516 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,740993253902877 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,74089215514231 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,739351324710469 )
J Chem Inf Model - Molecular determinants of Bim(BH3) peptide binding to pro-survival proteins. ( 0,7387910905865 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,736426146417497 )