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《核酸研究医学期刊》2003年第07期

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detection of reliable and unexpected protein fold predictions using 3d-jury
dsspcont: continuous secondary structure assignments for proteins
protinfo: secondary and tertiary protein structure prediction
the predictprotein server
genesilico protein structure prediction meta-server
meta-pp: single interface to crucial prediction servers
eva: evaluation of protein structure prediction servers
vadar: a web server for quantitative evaluation of protein structure quality
espript/endscript: extracting and rendering sequence and 3d information from atomic structures of proteins
webfeature: an interactive web tool for identifying and visualizing functional sites on macromolecular structures
3matrix and 3motif: a protein structure visualization system for conserved sequence motifs
motif3d: relating protein sequence motifs to 3d structure
loc3d: annotate sub-cellular localization for protein structures
annotation in three dimensions. pints: patterns in non-homologous tertiary structures
nci: a server to identify non-canonical interactions in protein structures
molsurfer: a macromolecular interface navigator
castp: computed atlas of surface topography of proteins
sem (symmetry equivalent molecules): a web-based gui to generate and visualize the macromolecules
servers for sequence-structure relationship analysis and prediction
pops: a fast algorithm for solvent accessible surface areas at atomic and residue level
matras: a program for protein 3d structure comparison
lga: a method for finding 3d similarities in protein structures
tools for comparative protein structure modeling and analysis
swiss-model: an automated protein homology-modeling server
sting millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
integrated databanks access and sequence/structure analysis services at the pbil
nrsas: nuclear receptor structure analysis servers
ssep: secondary structural elements of proteins
mfold web server for nucleic acid folding and hybridization prediction
rnasoft: a suite of rna secondary structure prediction and design software tools
pfold: rna secondary structure prediction using stochastic context-free grammars
vienna rna secondary structure server
pseudoviewer2: visualization of rna pseudoknots of any type
a software tool-box for analysis of regulatory rna elements
gprm: a genetic programming approach to finding common rna secondary structure elements
tools for the automatic identification and classification of rna base pairs
gepas: a web-based resource for microarray gene expression data analysis
inclusive: a web portal and service registry for microarray and regulatory sequence analysis
genepublisher: automated analysis of dna microarray data
expressyourself: a modular platform for processing and visualizing microarray data
chipinfo: software for extracting gene annotation and gene ontology information for microarray analysis
reduce: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
multiple sequence alignment with the clustal series of programs
cloure: clustal output reformatter, a program for reformatting clustalx/clustalw outputs for snp analysis and molecular systematics
tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
slam web server for comparative gene finding and alignment
theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
multipipmaker and supporting tools: alignments and analysis of multiple genomic dna sequences
mavid multiple alignment server
enterix 2003: visualization tools for genome alignments of enterobacteriaceae
mgalignit: a web service for the alignment of mrna/est and genomic sequences
revtrans: multiple alignment of coding dna from aligned amino acid sequences
promh: promoters identification using orthologous genomic sequences
fie2: a program for the extraction of genomic dna sequences around the start and translation initiation site of human genes
promoser: a large-scale mammalian promoter and transcription start site identification service
dragon gene start finder identifies approximate locations of the 5‘ ends of genes
etope: evolutionary test of predicted exons
siteseer: visualisation and analysis of transcription factor binding sites in nucleotide sequences
matchtm: a tool for searching transcription factor binding sites in dna sequences
gibbs recursive sampler: finding transcription factor binding sites
ymf: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
target explorer: an automated tool for the identification of new target genes for a specified set of transcription factors
regulatory sequence analysis tools
geneseqer@plantgdb: gene structure prediction in plant genomes
glimmerm, exonomy and unveil: three ab initio eukaryotic genefinders
dragon ere finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
patsearch: a program for the detection of patterns and structural motifs in nucleotide sequences
psort-b: improving protein subcellular localization prediction for gram-negative bacteria
signal search analysis server
mhcpred: a server for quantitative prediction of peptide-mhc binding
elm server: a new resource for investigating short functional sites in modular eukaryotic proteins
prediction of lipid posttranslational modifications and localization signals from protein sequences: big-, nmt and pts
scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
static benchmarking of membrane helix predictions
the web server of ibm‘s bioinformatics and pattern discovery group
identification of patterns in biological sequences at the alggen server: promo and malgen
searchpks: a program for detection and analysis of polyketide synthase domains
mak, a computational tool kit for automated mite analysis
cluster-buster: finding dense clusters of motifs in dna sequences
sic: a tool to detect short inverted segments in a biological sequence
mreps: efficient and flexible detection of tandem repeats in dna
spa: simple web tool to assess statistical significance of dna patterns
tracts: a program to map oligopurine.oligopyrimidine and other binary dna tracts
dna analysis servers: plot.it, bend.it, model.it and is
nebcutter: a program to cleave dna with restriction enzymes
svm-prot: web-based support vector machine software for functional classification of a protein from its primary sequence
bprompt: a consensus server for membrane protein prediction
globplot: exploring protein sequences for globularity and disorder
ispot: a web tool to infer the interaction specificity of families of protein modules
automated gene ontology annotation for anonymous sequence data
estannotator: a tool for high throughput est annotation
phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
amigene: annotation of microbial genes
dnannotator: annotation software tool kit for regional genomic sequences
bioverse: functional, structural and contextual annotation of proteins and proteomes
framed: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
eugène‘hom: a generic similarity-based gene finder using multiple homologous sequences
probemer: a web-based software tool for selecting optimal dna oligos
primer design assistant (pda): a web-based primer design tool
depie: designing primers for protein interaction experiments
oligodesign: optimal design of lna (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
codehop (consensus-degenerate hybrid oligonucleotide primer) pcr primer design
rna-related tools on the bielefeld bioinformatics server
sirw: a web server for the simple indexing and retrieval system that combines sequence motif searches with keyword searches
onto-tools, the toolkit of the modern biologist: onto-express, onto-compare, onto-design and onto-translate
swiss embnet node web server
expasy: the proteomics server for in-depth protein knowledge and analysis
uniqueprot: creating representative protein sequence sets
blast2srs, a web server for flexible retrieval of related protein sequences in the swiss-prot and sptrembl databases
wu-blast2 server at the european bioinformatics institute
ontoblast function: from sequence similarities directly to potential functional annotations by ontology terms
orfeus: detection of distant homology using sequence profiles and predicted secondary structure
parsesnp: a tool for the analysis of nucleotide polymorphisms
sift: predicting amino acid changes that affect protein function
actionmap: a web-based software that automates loci assignments to framework maps
web-thermodyn: sequence analysis software for profiling dna helical stability
newt, a new taxonomy portal
comprehensive quantitative analyses of the effects of promoter sequence elements on mrna transcription
pipealign: a new toolkit for protein family analysis
norsp: predictions of long regions without regular secondary structure
biological soap servers and web services provided by the public sequence data bank
footprinter: a program designed for phylogenetic footprinting
genefizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of dna sequences. gene discovery and evolutionary perspectives
geno2pheno: estimating phenotypic drug resistance from hiv-1 genotypes
building protein diagrams on the web with the residue-based diagram editor rbde
crp: cleavage of radiolabeled phosphoproteins
jvirgel: calculation of virtual two-dimensional protein gels
update on xplormed: a web server for exploring scientific literature
a hox gene mutation that triggers nonsense-mediated rna decay and affects alternative splicing during drosophila development
replication of damaged dna in vitro is blocked by p5
incision at hypoxanthine residues in dna by a mammalian homologue of the escherichia coli antimutator enzyme endonuclease v
concerted folding of a candida ribozyme into the catalytically active structure posterior to a rapid rna compaction
mitochondria-mediated nuclear mutator phenotype in saccharomyces cerevisiae
bacteriophage p1 ban protein is a hexameric dna helicase that interacts with and substitutes for escherichia coli dnab
pseudocomplementary pnas as selective modifiers of protein activity on duplex dna: the case of type iis restriction enzymes
the role of the yeast cleavage and polyadenylation factor subunit ydh1p/cft2p in pre-mrna 3‘-end formation
importance of the reverse hoogsteen base pair 54-58 for trna function
transient recruitment of the hnrnp k protein to inducibly transcribed gene loci
the cationic porphyrin tmpyp4 destabilizes the tetraplex form of the fragile x syndrome expanded sequence d(cgg)n
histone deacetylases in fungi: novel members, new facts
comparative protein structure modeling by iterative alignment, model building and model assessment
the frequency of gene targeting in trypanosoma brucei is independent of target site copy number
direct real-time molecular scale visualisation of the degradation of condensed dna complexes exposed to dnase i
initiation-mediated mrna decay in yeast affects heat-shock mrnas, and works through decapping and 5‘-to-3‘ hydrolysis
hfq affects the length and the frequency of short oligo(a) tails at the 3‘ end of escherichia coli rpso mrnas
processing of dna lesions by archaeal dna polymerases from sulfolobus solfataricus
spatial organization of topoisomerase i-mediated dna cleavage induced by camptothecin-oligonucleotide conjugates
region and amino acid residues required for rad51c binding in the human xrcc3 protein
the first completed genome sequence from a teleost fish (fugu rubripes) adds significant diversity to the nuclear receptor superfamily
the c terminus of the human telomerase reverse transcriptase is a determinant of enzyme processivity
cadlive for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
correlation between premeiotic dna replication and chromatin transition at yeast recombination initiation sites
sm-like proteins in eubacteria: the crystal structure of the hfq protein from escherichia coli
effect of dna target sequence on triplex formation by oligo-2‘-deoxy- and 2‘-o-methylribonucleotides
biochemical properties of phosphonoacetate and thiophosphonoacetate oligodeoxyribonucleotides
computational identification of non-coding rnas in saccharomyces cerevisiae by comparative genomics
an error-prone family y dna polymerase (dinb homolog from sulfolobus solfataricus) uses a steric gate residue for discrimination against ribonucleotides
unusual intercalation of acridin-9-ylthiourea into the 5‘-ga/tc dna base step from the minor groove: implications for the covalent dna adduct profile of a novel pl..
gaga facilitates binding of pleiohomeotic to a chromatinized polycomb response element
on the number of protein-protein interactions in the yeast proteome
selective interactions of human kin17 and rpa proteins with chromatin and the nuclear matrix in a dna damage- and cell cycle-regulated manner
chemical shift changes provide evidence for overlapping single-stranded dna- and xpa-binding sites on the 70 kda subunit of human replication protein a
mycobacterium tuberculosis reca intein, a laglidadg homing endonuclease, displays mn2+ and dna-dependent atpase activity
hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel rna secondary structure
leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a trna gene
thermodynamic calculations and statistical correlations for oligo-probes design
temperature-sensitive mutation in yeast mitochondrial ribosome recycling factor (rrf)
assessing functional divergence in ef-1 and its paralogs in eukaryotes and archaebacteria
unique actinomycin d binding to self-complementary d(cxyggccy‘x‘g) sequences: duplex disruption and binding to a nominally base-paired hairpin
the arabidopsis atlig4 gene is required for the repair of dna damage, but not for the integration of agrobacterium t-dna
formation of stable triplexes between purine rna and pyrimidine oligodeoxyxylonucleotides
molecular modeling of the chromatosome particle
molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between tar-tar and tar-aptamer
simultaneously monitoring dna binding and helicase-catalyzed dna unwinding by fluorescence polarization
streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice
mrna accessible site tagging (mast): a novel high throughput method for selecting effective antisense oligonucleotides
experimental validation of novel and conventional approaches to quantitative real-time pcr data analysis
a new thermus sp. class-iis enzyme sub-family: isolation of a twin endonuclease tspdti with a novel specificity 5‘-atgaa(n11/9)-3‘, related to tspgwi, taqii and t..
heteromeric mappit: a novel strategy to study modification-dependent protein-protein interactions in mammalian cells
simultaneous on/off regulation of transgenes located on a mammalian chromosome with cre-expressing adenovirus and a mutant loxp
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