J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ model(2220) cell(1177) simul(1124) }
{ network(2748) neural(1063) input(814) }
{ sampl(1606) size(1419) use(1276) }
{ bind(1733) structur(1185) ligand(1036) }
{ take(945) account(800) differ(722) }
{ first(2504) two(1366) second(1323) }
{ structur(1116) can(940) graph(676) }
{ problem(2511) optim(1539) algorithm(950) }
{ method(984) reconstruct(947) comput(926) }
{ data(1737) use(1416) pattern(1282) }
{ measur(2081) correl(1212) valu(896) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ perform(999) metric(946) measur(919) }
{ patient(2837) hospit(1953) medic(668) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ patient(2315) diseas(1263) diabet(1191) }
{ control(1307) perform(991) simul(935) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ model(3480) simul(1196) paramet(876) }
{ age(1611) year(1155) adult(843) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ use(976) code(926) identifi(902) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ imag(1057) registr(996) error(939) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ 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) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ 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) }
{ research(1085) discuss(1038) issu(1018) }
{ 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) }
{ 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) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ 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) }
{ 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) }
{ 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) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

We used cellular automata (CA) for the modeling of the temporal folding of proteins. Unlike the focus of the vast research already done on the direct prediction of the final folded conformations, we will model the temporal and dynamic folding process. To reduce the complexity of the interactions and the nature of the amino acid elements, lattice models like HP were used, a model that categorizes the amino acids regarding their hydrophobicity. Taking into account the restrictions of the lattice model, the CA model defines how the amino acids interact through time to obtain a folded conformation. We extended the classical CA models using artificial neural networks for their implementation (neural CA), and we used evolutionary computing to automatically obtain the models by means of Differential Evolution. As the iterative folding also provides the final folded conformation, we can compare the results with those from direct prediction methods of the final protein conformation. Finally, as the neural CA that provides the iterative folding process can be evolved using several protein sequences and used as operators in the folding of another protein with different length, this represents an advantage over the NP-hard complexity of the original problem of the direct prediction.

Resumo Limpo

use cellular automata ca model tempor fold protein unlik focus vast research alreadi done direct predict final fold conform will model tempor dynam fold process reduc complex interact natur amino acid element lattic model like hp use model categor amino acid regard hydrophob take account restrict lattic model ca model defin amino acid interact time obtain fold conform extend classic ca model use artifici neural network implement neural ca use evolutionari comput automat obtain model mean differenti evolut iter fold also provid final fold conform can compar result direct predict method final protein conform final neural ca provid iter fold process can evolv use sever protein sequenc use oper fold anoth protein differ length repres advantag nphard complex origin problem direct predict

Resumos Similares

Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,812740214851658 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,798953033998403 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,770847772595884 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,756371805838951 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,748828339696438 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,74399382487688 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,741986314406517 )
Comput Biol Chem - ISDTool: a computational model for predicting immunosuppressive domain of HERVs. ( 0,738280529023273 )
J. Comput. Biol. - Accurate estimations of evolutionary times in the context of strong CpG hypermutability. ( 0,73737763404771 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,737043355277768 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,736484660323524 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,734520381895354 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,733100574366362 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,732604455120493 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,724135513136668 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,724068136964825 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,723547168384833 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,721544634905938 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,718558341952661 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,715132072002178 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,709158958749701 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,708930769521595 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,708382231254367 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,708355476215764 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,707425476646795 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,706660257078891 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,706576709207735 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,704732124217216 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,698735647368966 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,697732670381331 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,697206807840872 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,695551245031828 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,695306901888235 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,69524172910067 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,694868066491003 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,694296802461789 )
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. ( 0,690534047199128 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,689962130913178 )
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. ( 0,689211411769861 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,688748209374314 )
J. Comput. Biol. - Learning cellular sorting pathways using protein interactions and sequence motifs. ( 0,686920264352823 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,685003138026961 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,684520244431475 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,684232757310296 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,682982136314266 )
Comput Math Methods Med - Inbuilt mechanisms for overcoming functional problems inherent in hepatic microlobular structure. ( 0,682964624242063 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,681066849464053 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,677184989306689 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,675541700524318 )
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. ( 0,674471929829182 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,673440477081098 )
Comput Math Methods Med - Dynamics of posttranslational modifications of p53. ( 0,67325967521167 )
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. ( 0,673042679219425 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,672487304298968 )
Comput Math Methods Med - Space constrained homology modelling: the paradigm of the RNA-dependent RNA polymerase of dengue (type II) virus. ( 0,667882028942876 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,667493084000936 )
IEEE Trans Pattern Anal Mach Intell - Spatiotemporal Alignment of Visual Signals on a Special Manifold. ( 0,667431021418596 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,666666932873275 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,666310078759656 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,665289842366084 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,664504392554679 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,663564620544053 )
J Chem Inf Model - Proteins as sponges: a statistical journey along protein structure organization principles. ( 0,661082234484221 )
J Biomed Inform - A kinetic model-based algorithm to classify NGS short reads by their allele origin. ( 0,660229182893681 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,659872366640614 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,659259213267571 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,65852001512734 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,657268308084204 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,656044560761717 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,655982032216963 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,655731801179336 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,655130224147047 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,653328581415292 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,653207900786454 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,649309916702447 )
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. ( 0,648737071097513 )
Comput Biol Chem - Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction. ( 0,646775710577519 )
J Chem Inf Model - Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. ( 0,646356823799688 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,646116188650682 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,646101929756019 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,645988109992007 )
Comput. Biol. Med. - A protein mapping method based on physicochemical properties and dimension reduction. ( 0,645311869812935 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,644984524070865 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,641884184588365 )
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. ( 0,641177820923263 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,640839508640359 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,638735170858779 )
J. Comput. Biol. - A probabilistic model of neutral and selective dynamics of protein network evolution. ( 0,63868960327533 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,637209302325581 )
J Chem Inf Model - Molecular determinants of Bim(BH3) peptide binding to pro-survival proteins. ( 0,636658059683911 )
J. Comput. Biol. - Detection of structural variants involving repetitive regions in the reference genome. ( 0,633679122054016 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,629507631486798 )
Comput Biol Chem - Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures. ( 0,62935984268818 )
Brief. Bioinformatics - Identify drug repurposing candidates by mining the protein data bank. ( 0,627317781325511 )
Comput Biol Chem - A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. ( 0,626841754821401 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,624627921253927 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,62434494277966 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,624192704589227 )
J. Comput. Biol. - Parallel continuous flow: a parallel suffix tree construction tool for whole genomes. ( 0,623899816939036 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,623802507294025 )