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A cognitive model for anaerobic digestion in fluidized bed reactors is developed. The general pathway of the process is divided into five main reactions performed by different bacterial groups. Molecular diffusion of each substrate involved in the reaction scheme is described. Effectiveness factor calculations are perf... |
The purification of industrial alpha-amylase by liquid-liquid extraction with Aliquat 336 reversed micellar solution as the extractant was studied. Seven kinds of Aliquat 336 reversed micellar solution, formed by using seven kinds of straight chain alkyl alcohols as cosolvent, have been utilized to extract industrial a... |
To determine the in vivo fluxes of the central metabolism we have developed a comprehensive approach exclusively based on the fundamental enzyme reactions known to be present, the fate of the carbon atoms of individual reactions, and the metabolite balance of the culture. No information on the energy balance is require... |
Recombinant human parvovirus B19 virus-like particles (VLPs), a candidate vaccine, were produced using the insect cell (Sf-9)-baculovirus (AcNPV) expression system. The synthesis and assembly of the particles in Sf-9 cells are directed by double infections with one recombinant virus (bacVP1) expressing the parvovirus m... |
The function of the reversible oxygen-binding hemoprotein from Vitreoscilla (VHb), which enhances oxygen-limited cell growth and recombinant protein production when functionally expressed in Escherichia coli, was investigated in wild-type E. coli and in E. coli mutants lacking one of the two terminal oxidases, cytochro... |
The use of expanded beds of STREAMLINE ion exchange adsorbents for the direct extraction of an intracellular enzyme glucose-6-phosphate dehydrogenase (G6PDH) from unclarified yeast cell homogenates has been investigated. It has been demonstrated that such crude feedstocks can be applied to the bed without prior clarifi... |
beta-Glycosidases catalyze the synthesis of glycosides when a nucleophilic acceptor other than water is present in the reaction medium. We describe the enzymatyc synthesis of 2-beta-D-galactopyranosyloxyethyl methacrylate (GalEMA) starting from 2-hydroxyethyl methacrylate (HEMA) and p-nitrophenyl-beta-D-galactopyranosi... |
The state of the art for upflow anaerobic sludge blanket (UASB) reactors is discussed, focusing on the microbiology of immobilized anaerobic bacteria and the mechanism of granule formation. The development of granular sludge is the key factor for successful operation of the UASB reactors. Criteria for determining if gr... |
The metabolic pathway and the properties of many of the enzymes involved in the citric acid biosynthesis in the mold Aspergillus niger are well known. This fact, together with the availability of new theoretical frameworks aimed at quantitative analyses of control and dynamics in metabolic systems, has allowed us to co... |
Hepatocytes isolated from male Fisher 344VF rats were cultured on two substrates, collagen I and a lactose-derivatized polystyrene (PS-lactose), to compare morphological and functional differences. Hepatocyte morphology changed dramatically depending upon the substrate, shown through actin cytoskeletal staining and sca... |
Relatively conservative modifications of three proteins were carried out to alter their surface properties. The protein properties modified were hydrophobicity and charge. This was done by acylation of amino groups with anhydrides. For the hydrophobic modification experiments, two proteins (beta-lactoglobulin and bovin... |
Two different series of hydrophobically modified proteins were partitioned in a number of aqueous two-phase systems (ATPS) to investigate the effect of hydrophobicity as a single property on partitioning. The modified proteins were derived from beta-lactoglobulin and bovine serum albumin (BSA). Measurement of the surfa... |
A series of charge-modified thaumatins with different values of surface charge were partitioned in aqueous two-phase systems (ATPS) to study the effect of surface charge as a single property on partitioning. Electrophoretic mobility of the proteins in titration curves was used as a measure of surface charge. Four modif... |
Bioprocess identification starts with collection of process information. Usually there is a variety of information available, consisting of actual measurement data, historical data, empirical kinetic and yield correlations, and general knowledge available from literature. A central problem is to find out how the variou... |
The c-fos protein belongs to a family of transcriptional cofactors that can complex with proteins of the Jun family and activate mRNA transcription from gene promoters containing an activator protein 1 (AP-1) binding element. The shear stress inducibility of the c-fos protein was studied in human and animal cell lines ... |
The macro-kinetic behavior of phenol removal from a synthetic exhaust gas was investigated theoretically as well as experimentally by means of two identical continuously operating laboratory-scale biological filter bed columns. A mixture of peat and glass beads was used as filter material. After sterilization it was in... |
We studied a model transesterification reaction catalyzed by subtilisin Carlsberg suspended in carbon dioxide, propane, and mixtures of these solvents under pressure. To account for solvent effects due to differences in water partitioning between the enzyme and the bulk solvents, we measured water sorption isotherms fo... |
The precipitation equilibria of hen egg-white lysozyme and bovine serum albumin from aqueous solutions by caprylic acid were studied. A thermodynamic equilibrium was obtained, and the compositions of both the precipitate and the aqueous phases were measured to establish phase diagrams for both systems. The precipitate ... |
Two Escherichia coli strains, widely used for the production of various recombinant proteins, were compared for their pre-induction growth and acetate accumulation patterns. The strains studied were E. coli BL21 (lambdaDE3), transformed with a plasmid encoding Pseudomonas exotoxin A, and an E. coli K12 derived strain, ... |
Biotransformation of benzaldehyde to L-phenylacetylcarbinol (L-PAC) as a key intermediate for L-ephedrine has been evaluated using immobilized pyruvate decarboxylase (PDC) from Candida utilis. PDC immobilized in spherical polyacrylamide beads was found to have a longer half-life compared with free enzyme. In a batch pr... |
A phenomenological model of biocide action against microbial biofilms was derived. Processes incorporated in the model include bulk flow in and out of a well-mixed reactor, transport of dissolved species into the biofilm, substrate consumption by bacterial metabolism, bacterial growth, advection of cell mass within the... |
Hepatoblastoma (HB), the most common pediatric malignant liver tumor, is treated with chemotherapy to facilitate surgical resection. Previous studies suggest that HB acquires chemoresistance via increased expression of multidrug resistance protein 1 (MDR1, ABCC1). There is no well established evidence that this also oc... |
Chondrosarcomas are highly resistant to conventional radiation and chemotherapy, and surgical removal is the only option for curative treatment. Consequently, there is nothing to offer patients with inoperable tumours and metastatic disease. The aim of this study is to investigate genes involved in cell cycle control: ... |
Human endothelial nitric oxide synthase (eNOS) plays a pivotal role in maintaining blood pressure homeostasis and vascular integrity. It has recently been reported that mitogen-activated protein kinases (MAPKs) are intimately implicated in expression of eNOS. However detailed mechanism mediated by them remains to be cl... |
Pharmacological GSK-3 inhibitors are potential drugs for the treatment of neurodegenerative diseases, cancer and diabetes. We examined the antiproliferative effects of two GSK-3 inhibitors, lithium and SB-415286, on B65 neuroblastoma cell line. Treatment of B65 cells with either drug administered separately caused a de... |
The purpose of the present study was to determine the relative amount of S-thiolated proteins (i.e. S-homocysteinylated, S-cysteinylglycinylated, S-glutathionylated and S-cysteinylated proteins) to the total protein thiols (i.e. the sum of reduced protein sulphydryl groups (PSHs) and protein mixed disulphides with homo... |
Oxidation and glycation of low-density lipoprotein (LDL) promote vascular injury in diabetes; however, the mechanisms underlying this effect remain poorly defined. The present study was conducted to determine the effects of 'heavily oxidized' glycated LDL (HOG-LDL) on endothelial nitric oxide synthase (eNOS) function. ... |
Autism spectrum disorders (ASD) comprise a complex and heterogeneous group of conditions of unknown aetiology, characterized by significant disturbances in social, communicative and behavioural functioning. Recent studies suggested a possible implication of the high-density lipoprotein associated esterase/lactonase par... |
Steam-exploded corn stover biomass was used as the substrate for fed-batch separate enzymatic hydrolysis and fermentation (SHF) to investigate the solid concentration ranging from 10% to 30% (w/w) on the lignocellulose enzymatic hydrolysis and fermentation. The treatment of washing the steam-exploded material was also ... |
The impact of influent dissolved O(2) on the characteristics of anaerobic granular sludge was investigated at various dissolved O(2) concentrations (0.5-8.1 ppm) in 1- and 5-L laboratory-scale upflow anaerobic sludge bed (UASB)-like anaerobic/aerobic coupled reactors with a synthetic wastewater (carbon sources containi... |
In vitro infection of insect cells with baculoviruses is increasingly considered a viable means for the production of biopesticides, recombinant veterinary vaccines, and other recombinant products. Batch fermentation processes traditionally employ intermediate to high multiplicities of infection necessitating two paral... |
A structured model of substrate-utilization kinetics that encompasses dual-limitation conditions, caused by simultaneously low concentrations of the electron donor and the electron acceptor, is developed by incorporating the internal cofactor responses into the kinetic variables. The structured model is based on an ass... |
The highly systematic responses of cellular cofactors to controlled substrate limitations of electron donor, electron acceptor, and both (dual limitation) were quantified using continuous-flow cultures of Pseudomonas putida. The results showed that the NADH concentration in the cells decreased gradually as the specific... |
The adsorption of water by alcohol dehydrogenase from baker's yeast (YADH) has been measured in a continuous-flow gas reactor at varying temperatures. Adsorption isotherms in the presence of gaseous organic substrates are compared to those from organic-free gas mixtures. Almost no effect of the hydrophobic molecule on ... |
The degree of enzyme hydration is the one of the most important factors which can affect enzyme activity and stability in water-limited environments. Alcohol dehydrogenase from baker's yeast (YADH) has been used as a model enzyme to study the effects of hydration on activity, stability, and cofactor stability with gas ... |
The characteristics and development of thermophilic anaerobic sludge in upflow staged sludge bed (USSB) reactors were studied. The compartmentalized reactors were inoculated with partially crushed mesophilic granular sludge and then fed with either a mixture of volatile fatty acids (VFA) or a mixture of sucrose and VFA... |
A rigorous dynamic mathematical model for predicting the rate of ultrafiltration of proteins has been developed. The model is based on sophisticated descriptions of the protein-protein interactions within the layer close to the membrane surface which are responsible for controlling permeation rate. Electrostatic intera... |
The aggregation of biotin-modified phospholipid vesicles (liposomes) induced by binding the protein avidin in solution is analyzed experimentally and theoretically. Avidin has four binding sites that can recognize biotin specifically, and is able to cross-link the liposomes to form large aggregates. The aggregation kin... |
The aggregation of biotinylated phospholipid vesicles (liposomes) cross-linked by antibiotin IgG was studied experimentally and theoretically. The liposomes were either low density liposomes that contained 0.4 mol% biotinylated phospholipid ( approximately 100 exposed biotin molecules per liposome), or high density lip... |
The specific secretion rate (q, microg protein secreted/viable cell-h) and its variance are very useful to compare the capability of cell lines for protein secretion. An assessment of specific secretion rate variability is also beneficial and important when the specific secretion rate is to be used as an on-line proces... |
The reverse micellar system of sodium bis(2-ethylhexyl) phosphate (NaDEHP)/isooctane/brine was used for liquid-liquid extraction of proteins. We investigated the solubilization of cytochrome-c and alpha-chymotrypsin into the NaDEHP reverse micellar phase by varying the pH and NaCl concentration in the aqueous phase. At... |
The effect of a quiescent microgravity fluid environment on the activity of collagenase directed at demineralized bone fragments was investigated over a period of 10 days. Enzyme treatment resulted in greater mass loss in microgravity, with nearly three times the loss of mass during Space Shuttle mission STS-62 compare... |
The present studies were undertaken to evaluate the in vitro gel stability of the hydrogels alginate and agarose. Gel strength (of alginate and agarose) and protein diffusion (of alginate only) were shown to correlate with gel stability and to be useful techniques to monitor gel stability over time. The gel strengths o... |
We investigated the migration of rat calvaria osteoblast populations on poly(alpha-hydroxy ester) films for up to 14 days to determine effects of substrate composition and culture conditions on the migratory characteristics of osteoblasts. Initial osteoblast culture conditions included cell colonies formed by seeding a... |
CD8(+) cytotoxic T-lymphocytes (CTLs) have been proven, in multiple animal models, to be the most powerful antiviral and antitumor components of the immune system. We have developed a protocol to activate and expand tumor and virus peptide-specific CD8(+) T-lymphocytes from the peripheral blood of healthy, human trophi... |
Continuous, single-step, state-of-the-art preparative separations of enzymes from microorganism crude extracts by free-flow zone electrophoresis are presented. In the first example, the enzymes formate dehydrogenase, formaldehyde dehydrogenase, and methanol oxidase were continuously separated from Candida boidinii crud... |
A novel technique is described for the immobilization of Candida cylindracea lipase in the soapy-shell of colloidal liquid aphrons (CLAs). CLAs consist of a micron-sized solvent droplet surrounded by a thin, aqueous, soapy-film and are stabilized by a mixture of nonionic and ionic surfactants. Retention of lipase withi... |
There are a series of examples in which phenols appear as contaminants in process streams and their selective removal is required for waste minimization. For the selective removal of a phenol from a mixture, we are exploiting the substrate specificity of the enzyme tyrosinase to convert phenols into reactive o-quinones... |
The kinetics of utilization of glucose, phenol, and their mixtures by Pseudomonas putida (ATCC 17514) were studied with a continuously aerated, jacketed batch reactor operating at 28 degrees C and pH 7.2. It was found that when glucose is the sole carbon and energy source, the culture utilizes it following Monod kineti... |
The enantioselectivities of subtilisin Carlsberg and Rhizomucor miehei lipase in organic solvents are found to strongly depend on the method by which the enzymes are prepared. For the transesterification between sec-phenethyl alcohol and vinyl butyrate in dioxane at 7 degrees C, the enantioselectivity of subtilisin pre... |
Self-cycling fermentation (SCF) in a stirred tank reactor was applied to the biodegradation of phenol by Pseudomonas putida. The technique resulted in stable and repeatable performance. Complete substrate consumption was achieved under all operating conditions investigated. SCF resulted in substrate utilization rates a... |
Immobilization of horseradish peroxidase on magnetite and removal of chlorophenols using immobilized enzyme were investigated. Immobilization by physical adsorption on magnetite was much more effective than that by the crosslinking method, and the enzyme was found to be immobilized at 100% of retained activity. In addi... |
Although the necessity of divalent magnesium and manganese for full activity of sugar nucleotidyltransferases and glycosyltransferases is well known, the role of these metal cations in binding the substrates (uridine 5'-triphosphate, glucose-1-phosphate, N-acetylglucosamine-1-phosphate, and uridine 5'-diphosphate gluco... |
Hexactinellids are deep water sponges that possess syncytial rather than cellular tissues. In order to investigate the syncytial character of the tissue of these unusual sponges, primary cultures were developed using a substrate of acellular tissue extract (ATE) that promotes the adhesion and spreading of sponge tissue... |
The electron microscopical changes in the glial lacunar network that surrounds the large neurons of meso- and metacerebrum of land snail cerebral ganglia were considered, in order to get an insight into the functional role of this peculiar structure in invertebrates. Compared with snails during the active period, in th... |
Cadmium (Cd) pathology was studied in an insect cell line (Aedes albopictusC6/36) at the ultrastructural level. The most prominent pathological changes occurred at the level of the nucleus: chromatin clumping, indentations, filling and dilatation of the perinuclear cisternae and an increased amount of bound ribosomes w... |
The proteins that make up arthropod gap and septate junctions have not been identified with any certainty. Several candidate proteins for both types of junctions have been proposed in the literature, but there has been no agreement on any of these. Arthropod gap junctions do not label with antibodies to vertebrate gap ... |
Abstract.The ultrastructural effects of mercuric chloride (Hg) and methylmercuric chloride (MeHg) were studied in theAedes albopictusC6/36 cell line. Both metal salts caused nuclear indentations, chromatin clumping and proliferation of the nucleolus. The mitochondria became pleomorphous. An increase of both free and me... |
Ultrastructural cytochemical techniques were used for the localization of phosphatases and oxidases in spermatid and spermatozoon of the phytophagous bugs Acrosternum aseadum and Nezara viridula (Hemiptera: Pentatomidae). Acid phosphatase was found mainly in the trans most portion of the Golgi complex, and in the acros... |
Progress is reviewed towards the development of a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of high performance separations and mass spectrometry. The approach uses high accuracy mass measurements from Fourier transf... |
The goal of the Plant Ontology Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa (e.g. development, anatomy, morphology, genomics, proteomics) is accumulating and changi... |
In the post-genomic era, validation of candidate gene targets frequently requires proteinbased strategies. Phage display is a powerful tool to define protein-protein interactions by generating peptide binders against target antigens. Epitope phage display libraries have the potential to enrich coding exon sequences fro... |
In recent months a bumper crop of genomes has been completed, including the fission yeast (Schizosaccharomyces pombe) and rice (Oryza sativa). Two large-scale studies of Saccharomyces cerevisiae protein complexes provided a picture of the eukaryotic proteome as a network of complexes. Amongst the other stories of inter... |
The Industrialization Workshop Series aims to promote and discuss integration, automation, simulation, quality, availability and standards in the high-throughput life sciences. The main issues addressed being the transformation of bioinformatics and bioinformaticsbased drug design into a robust discipline in industry, ... |
A combination of surface plasmon resonance (SPR) and matrix-assisted laser-desorptionionization- time-of-flight mass spectrometry (MALDI-TOF-MS) was used to study the interaction between endopolygalacturonase (PG) from Fusarium moniliforme and a polygalacturonase-inhibiting protein (PGIP) from Phaseolus vulgaris. PG hy... |
Historically genotypic variation has been detected at the phenotypic level, at the metabolic level, and at the protein chemistry level. Advances in technology have allowed its direct visualisation at the level of DNA variation. Nevertheless, there is still an enormous interest in phenotypic, metabolic and protein prope... |
Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and... |
A relational database structure based on MS-Access and MySQL to store and manage proteomics data was established. This system may be used to publish two-dimensional electrophoretic proteomics data, and also may be accessed by external users who want to compare their own data with those in the databases. The maintenance... |
Bioinformatic tools have become essential to biologists in their quest to understand the vast quantities of sequence data, and now whole genomes, which are being produced at an ever increasing rate. Much of these sequence data are single-pass sequences, such as sample sequences from organisms closely related to other o... |
Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the obs... |
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate predict... |
The Dictionary of Interacting Proteins (DIP) (Xenarios et al., 2000) is a large repository of protein interactions: its March 2000 release included 2379 protein pairs whose interactions have been detected by experimental methods. Even if many of these correspond to poorly characterized proteins, the result of massive y... |
Yeast deletion strains created during gene function analysis projects very often show drastic phenotypic differences depending on the genetic background used. These results indicate the existence of important molecular differences between the CEN.PK2, FY1679 and W303 wild type strains. To characterise these differences... |
Obligate intracellular bacteria commonly have much reduced genome sizes compared to their nearest free-living relatives. One reason for this is reductive evolution: the loss of genes rendered non-essential due to the intracellular habitat. This can occur because of the presence of orthologous genes in the host, combine... |
Lymphocytes are the best-studied higher eukaryote cells. In this report, quantitative relationships of the protein components in resting cell, blast cell and plasma cell types are evaluated. The comparison of these cell types leads to the conclusion that resting cells synthesize about one-twentieth of the protein speci... |
Structural genomics strives to represent the entire protein space. The first step towards achieving this goal is by rationally selecting proteins whose structures have not been determined, but that represent an as yet unknown structural superfamily or fold. Once such a structure is solved, it can be used as a template ... |
Many vaccines have been developed from live attenuated forms of bacterial pathogens or from killed bacterial cells. However, an increased awareness of the potential for transient side-effects following vaccination has prompted an increased emphasis on the use of sub-unit vaccines, rather than those based on whole bacte... |
Cardiac remodelling with interstitial fibrosis in renal failure, which so far is only poorly understood on the molecular level, was investigated in the rat model by a global gene expression profiling analysis. Sprague-Dawley rats were subjected to subtotal nephrectomy (SNX) or sham operation (sham) and followed for 2 a... |
We describe the cloning, sequencing and structure of the human fast skeletal troponin T (TNNT3) gene located on chromosome 11p15.5. The single-copy gene encodes 19 exons and 18 introns. Eleven of these exons, 1-3, 9-15 and 18, are constitutively spliced, whereas exons 4-8 are alternatively spliced. The gene contains an... |
The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve ortholo... |
An increasing number of groups are now working in the area of text mining, focusing on a wide range of problems and applying both statistical and linguistic approaches. However, it is not possible to compare the different approaches, because there are no common standards or evaluation criteria; in addition, the various... |
The purpose of this short article is to examine certain aspects of protein functionality with relation to some key organizing ideas. This is important from a computational viewpoint in order to take account of modelling both biological systems and knowledge of these systems. We look at some of the lexical dimensions of... |
Interactions between proteins are essential for intracellular communication. They form complex networks which have become an important source for functional analysis of proteins. Combining phylogenies with network analysis, we investigate the evolutionary history of interaction networks from the bHLH, NR and bZIP trans... |
We describe a probabilistic peptide fragmentation model for use in protein databank searching and de novo sequencing of electrospray tandem mass spectrometry data. A probabilistic framework for tuning of the model using a range of well-characterized samples are introduced. We present preliminary results of our tuning e... |
We have identified four novel repeats and two domains in cell surface proteins encoded by the Methanosarcina acetivorans genome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conser... |
A small group of around 40 people came together at the Chancellors Conference Centre in Manchester for the Ontologies Workshop, chaired by Alan Rector and Robert Stevens. The workshop was, rather strangely, spread over 2 half days. In hindsight, this programme worked very well as it gave people the opportunity to chat ... |
A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characte... |
In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts of new data that need to be carefully analysed to obtain correct an... |
This short review comments on current informatics resources and methodologies in the study of functional pathways in cell biology. It highlights recent achievements in unveiling the structural design of protein and gene networks and discusses current approaches to model and simulate the dynamics of regulatory pathways ... |
The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle f... |
DNA arrays were used to measure changes in transcript levels as yeast cells responded to temperature shocks. The number of genes upregulated by temperature shifts from 30 to 37 or 45 was correlated with the severity of the stress. Pre-adaptation of cells, by growth at 37 previous to the 45 shift, caused a decrease in t... |
This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived ... |
Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks. |
Proteins perform many of their biological roles through protein-protein, protein-DNA or protein-ligand interfaces. The identification of the amino acids comprising these interfaces often enhances our understanding of the biological function of the proteins. Many methods for the detection of functional interfaces have b... |
Ab initio prediction is the challenging attempt to predict protein structures based only on sequence information and without using templates. It is often divided into two distinct sub-problems: (a) the scoring function that can distinguish native, or native-like structures, from non-native ones; and (b) the method of s... |
Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinit... |
Protein interactions are central to most biological processes, and are currently the subject of great interest. Yet despite the many recently developed methods for interaction discovery, little attention has been paid to one of the best sources of data: complexes of known three-dimensional (3D) structure. Here we discu... |
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts used and a common need to capture experimental information in a standardized manner. In building the MGED ontology, it was ... |
Fungal phytopathogens continue to cause major economic impact, either directly, through crop losses, or due to the costs of fungicide application. Attempts to understand these organisms are hampered by a lack of fungal genome sequence data. A need exists, however, to develop specific bioinformatics tools to collate and... |
We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. ... |
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