proteins

..The composite score had successful prediction for 13 of the 15 antibody-antigen targets...

..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...

..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...

..Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a ..

..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...

..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...

..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)...

..data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files...

..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource...

..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...

..The method is implemented as a public WWW service...

Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation...

..Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of ..

..Rictor-mTOR may serve as a drug target in tumors that have lost the expression of PTEN, a tumor suppressor that opposes Akt/PKB activation...

..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...

..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...

..nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, ..

..with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP...

..We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html...

..DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca...

..We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function ..

A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample...

..Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations...

..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...

In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale...

HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs)...

..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...

..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...

Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication...

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..3 million proteins organized into 42.7 million pairwise ortholog groups...

..family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as ..

..Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict ..

Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e...

..Glide is also found to be more accurate than the recently described Surflex method...

..This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates...

..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...

We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution...

..Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008...

Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions...

..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins...

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..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...

..Here, we show that wild-type Bcl-2 antiapoptotic proteins, but not Beclin 1 binding defective mutants of Bcl-2, inhibit Beclin 1-dependent autophagy in yeast and mammalian ..

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..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions...

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships...

..In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 A backbone RMSD)...

..This was also the case for 46 proteins in a mouse whole cell lysate...

Acetylation of proteins on lysine residues is a dynamic posttranslational modification that is known to play a key role in regulating transcription and other DNA-dependent nuclear processes...

In-gel digestion of proteins isolated by gel electrophoresis is a cornerstone of mass spectrometry (MS)-driven proteomics. The 10-year-old recipe by Shevchenko et al. has been optimized to increase the speed and sensitivity of analysis...

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..complexes that are highly coherent in terms of the function, expression and conservation of their member proteins. Importantly, we apply our method to study three multi-factorial diseases for which some causal genes have been ..

..We show that amino acids induce the movement of mTORC1 to lysosomal membranes, where the Rag proteins reside...

..that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids...

..We present a method for detecting distant homologous relationships between proteins based on this approach...

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..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...

..A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign...

..1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of ..

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions...

The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database...

..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...

Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing...

..GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, ..

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem...

..The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data ..

..Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website...

..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...

..We find that the Rag proteins--a family of four related small guanosine triphosphatases (GTPases)--interact with mTORC1 in an amino acid-..

..The force field shows improvement in redocking simulations over the previous AutoDock3 force field...

..We summarize recent experimental data and the resulting insights into allostery within proteins, and we discuss the nature of future studies and the new applications that may result from increased ..

..These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic ..

..With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence ..

..Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database...

..In the presence of survival factors, Akt phosphorylates FKHRL1, leading to FKHRL1's association with 14-3-3 proteins and FKHRL1's retention in the cytoplasm...

..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...

A protein interaction network describes a set of physical associations that can occur between proteins. However, within any particular cell or tissue only a subset of proteins is expressed and so only a subset of interactions can occur...

..The nodes of these networks are usually proteins (specifically enzymes in metabolic networks), whereas the links (or edges) are their interactions with other ..

..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models...

..To perform this analysis, an ANN has been trained on a set of 55 proteins, searching for a relation between protein fragments modeled by 13alpha torsion angles and the residue ..

..The operations of the FAMS algorithm are fully automated, and, therefore, special knowledge, techniques or experience are not required in order to obtain a biologically worthwhile protein structure...

..We have paid attention to ensure that fold-space is properly sampled, that the structures involved in alignments are of significant resolution (better than 2.5 A) and the alignments are accurate and reliable...

..The lowest energy docked conformations are generally associated with near-native conformations, less than 3.0 Angstrom dRMS (and in many cases less than 1.0 Angstrom) from the experimentally determined structures...

Current approaches to contact map prediction in proteins have focused on amino acid conservation and patterns of mutation at sequentially distant positions...

A number of equally optimal alignments inherently exist in the sequence and structure comparisons among proteins. To represent the sub-optimal alignments systematically, we have developed a method of generating probabilistic alignments ..

..In other words, the conflict between specific interactions between small numbers of biomolecules and weak, nonspecific interaction with the rest need not be a very serious design constraint...

b>Proteins can exist in at least three forms: the ordered form (solid-like), the partially folded form (collapsed, molten globule-like or liquid-like) and the extended form (extended, random coil-like or gas-like)...

..Relaxation into the globular ground state shows a weak power-law decay, i.e., R(g) proportional, variant t(-alpha) , alpha approximately 0.06-0.12 ...

..This stretch, which may be only structured transiently in the isolated molecule, could play a major role in Grb14 PIR binding to a biological partner by undergoing a structural transition...

We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced Calpha and side-..

..HEV32 provides a simple molecular model for studying protein-carbohydrate interactions and for understanding the physiological relevance of small native hevein domains lacking C-terminal residues...

..Such internal motif identified in this study suggests a new type of sequence motif recognition for Dvl PDZ domain...

..Statistical models have been developed for sequence-structure correlations in proteins at five levels of structural complexity: (i) short motifs; (ii) extended motifs; (iii) nonlocal pairs of motifs; (..

Prediction of topological representations of proteins that are geometrically invariants can contribute towards the solution of fundamental open problems in structural genomics like folding...

..We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful...

..g., ligand binding) and mutations. The PMR morph movies and statistics can be freely viewed from the PMR website, http://pmr.sdsc.edu...

..GST peptides with these amino acids will be used to isolate proteins that recognize these motifs...

..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...

..phospholipids to form a phosphatidylserine (PS)-rich exofacial surface, expression and insertion of fusion proteins into the plasma membrane, and rearrangement of actin cytoskeletal elements...

..phospholipids to form a phosphatidylserine (PS)-rich exofacial surface, expression and insertion of fusion proteins into the plasma membrane, and rearrangement of actin cytoskeletal elements...

..endo-/exocytotic compartments in 3T3-L1 adipocytes including vesicles which transport membrane associated proteins like GLUT4, secreted proteins where secretion is stimulated by insulin such as ARCP30 (adipocyte complement ..

..terminal repeat retrotransposon in budding yeast containing GAG3 and POL3 ORFs encoding structural and catalytic proteins, respectively...

Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...

Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...

Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...

..Working against this process is nucleotide excision repair (NER) of the adducts. The binding of cellular proteins, such as HMGB1, to DNA across from cisplatin cross-links shields them from NER and sensitizes cells to the drug...

..Most of the research proposal is an investigation of the proteins and protein binding sites required for these two waves of transcriptional activation...

..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas' disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...

..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas' disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...

Brucella melitensis, an intracellular human pathogen, is largely controlled by CD8+ T cells, but the Brucella proteins containing peptides recognized by protective CD8+ T cells remain unknown...

Brucella melitensis, an intracellular human pathogen, is largely controlled by CD8+ T cells, but the Brucella proteins containing peptides recognized by protective CD8+ T cells remain unknown...

..biochemical analyses, for the last fifteen years the prevailing view has been that Pbx/Exd primarily helps Hox proteins execute their developmental programs. Hence, Pbx proteins have been named as "Hox cofactors"...

We have discovered a series of heme proteins in the saliva of the blood-sucking bug Rhodnius prolixus that act as vasodilators, anti-platelet aggregation and anti-histaminic agents when injected into the victim...

..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas'disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...

..The core contains the viral DNA and at least 50 viral proteins. Core substructures can be distinguished by electron microscopy, including lateral bodies, a core wall, and a ..

..During the requested funding period, we propose to develop structural assembly of multi-domain proteins associated with intrinsic blood coagulation pathway...