Genomes and Genes
Summary: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Publications276 found, 100 shown here
- Incorporating intermolecular distance into protein-protein dockingHongxing Lei
UC Davis Genome Center and Bioinformatics Program, Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616, USA
Protein Eng Des Sel 17:837-45. 2004..The composite score had successful prediction for 13 of the 15 antibody-antigen targets...
- ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteinsMarkus Wiederstein
Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
Nucleic Acids Res 35:W407-10. 2007..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
- Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignmentsGerard Talavera
Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
Syst Biol 56:564-77. 2007..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
- The quest for orthologs: finding the corresponding gene across genomesArnold Kuzniar
Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
Trends Genet 24:539-51. 2008..Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a ..
- iRefIndex: a consolidated protein interaction database with provenanceSabry Razick
The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
BMC Bioinformatics 9:405. 2008..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...
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsS F Altschul
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 25:3389-402. 1997..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
- KEGG: kyoto encyclopedia of genes and genomesM Kanehisa
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 28:27-30. 2000..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)...
- InterPro: the integrative protein signature databaseSarah Hunter
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nucleic Acids Res 37:D211-5. 2009..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...
- The Protein Data BankH M Berman
Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
Nucleic Acids Res 28:235-42. 2000..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...
- The IntAct molecular interaction database in 2010B Aranda
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 38:D525-31. 2010..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...
- Inference of macromolecular assemblies from crystalline stateEvgeny Krissinel
European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
J Mol Biol 372:774-97. 2007..The method is implemented as a public WWW service...
- STRING 8--a global view on proteins and their functional interactions in 630 organismsLars J Jensen
European Molecular Biology Laboratory, Heidelberg, Germany
Nucleic Acids Res 37:D412-6. 2009Functional 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...
- CDD: a Conserved Domain Database for the functional annotation of proteinsAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 39:D225-9. 2011..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 ..
- Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complexD D Sarbassov
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
Science 307:1098-101. 2005..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 enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantificationJürgen Cox
Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
Nat Biotechnol 26:1367-72. 2008..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: all-atom contacts and structure validation for proteins and nucleic acidsIan W Davis
Department of Biochemistry, Duke University, Durham, NC, USA
Nucleic Acids Res 35:W375-83. 2007MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...
- BLAT--the BLAST-like alignment toolW James Kent
Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Genome Res 12:656-64. 2002..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...
- NCBI Reference Sequences: current status, policy and new initiativesKim D Pruitt
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 4As 47B, 45 Center Drive, Bethesda, MD, USA
Nucleic Acids Res 37:D32-6. 2009..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, ..
- The Amber biomolecular simulation programsDavid A Case
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
J Comput Chem 26:1668-88. 2005..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.
- Improved prediction of signal peptides: SignalP 3.0Jannick Dyrløv Bendtsen
Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
J Mol Biol 340:783-95. 2004We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP...
- SIFT: Predicting amino acid changes that affect protein functionPauline C Ng
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A1-162, Seattle, WA 98109, USA
Nucleic Acids Res 31:3812-4. 2003..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: a knowledgebase for drugs, drug actions and drug targetsDavid S Wishart
Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
Nucleic Acids Res 36:D901-6. 2008..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...
- Human non-synonymous SNPs: server and surveyVasily Ramensky
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 30:3894-900. 2002..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 for identifying proteins by tandem mass spectrometryAlexey I Nesvizhskii
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
Anal Chem 75:4646-58. 2003A 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...
- Reactome knowledgebase of human biological pathways and processesLisa Matthews
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
Nucleic Acids Res 37:D619-22. 2009..Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations...
- The GOA database in 2009--an integrated Gene Ontology Annotation resourceDaniel Barrell
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 37:D396-403. 2009..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...
- PANTHER: a library of protein families and subfamilies indexed by functionPaul D Thomas
Protein Informatics, Celera Genomics, Foster City, California 94404, USA
Genome Res 13:2129-41. 2003In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale...
- Identification of host proteins required for HIV infection through a functional genomic screenAbraham L Brass
Department of Genetics, Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
Science 319:921-6. 2008HIV-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)...
- Initial sequencing and analysis of the human genomeE S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- PID: the Pathway Interaction DatabaseCarl F Schaefer
National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
Nucleic Acids Res 37:D674-9. 2009..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...
- Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replicationRenate König
Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 135:49-60. 2008Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication...
- Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locusS Srinivas
Department of Genetics and Development, Columbia University, New York, USA
BMC Dev Biol 1:4. 2001....
- InParanoid 7: new algorithms and tools for eukaryotic orthology analysisGabriel Ostlund
Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
Nucleic Acids Res 38:D196-203. 2010..3 million proteins organized into 42.7 million pairwise ortholog groups...
- An efficient algorithm for large-scale detection of protein familiesA J Enright
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 30:1575-84. 2002..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 ..
- Locating proteins in the cell using TargetP, SignalP and related toolsOlof Emanuelsson
Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
Nat Protoc 2:953-71. 2007..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 ..
- iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteinsKuo Chen Chou
Gordon Life Science Institute, San Diego, California, United States of America
PLoS ONE 6:e18258. 2011Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e...
- Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracyRichard A Friesner
Department of Chemistry, Columbia University, New York, New York 10036, USA
J Med Chem 47:1739-49. 2004..Glide is also found to be more accurate than the recently described Surflex method...
- A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approachS Whelan
Department of Zoology, University of Cambridge, Cambridge, England
Mol Biol Evol 18:691-9. 2001..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...
- Comparison of multiple Amber force fields and development of improved protein backbone parametersViktor Hornak
Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
Proteins 65:712-25. 2006..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...
- Imaging intracellular fluorescent proteins at nanometer resolutionEric Betzig
Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA 20147, USA
Science 313:1642-5. 2006We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution...
- Infrastructure for the life sciences: design and implementation of the UniProt websiteEric Jain
Swiss Prot group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
BMC Bioinformatics 10:136. 2009..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...
- IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy contentZsuzsanna Dosztanyi
Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
Bioinformatics 21:3433-4. 2005Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions...
- AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMRR A Laskowski
Department of Biochemistry and Molecular Biology, University College London, UK
J Biomol NMR 8:477-86. 1996..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
- A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculationsYong Duan
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
J Comput Chem 24:1999-2012. 2003Molecular 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...
- The role of dynamic conformational ensembles in biomolecular recognitionDavid D Boehr
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
Nat Chem Biol 5:789-96. 2009....
- The evolutionary fate and consequences of duplicate genesM Lynch
Department of Biology, University of Oregon, Eugene, OR 97403, USA
Science 290:1151-5. 2000..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...
- Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagySophie Pattingre
Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
Cell 122:927-39. 2005..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 ..
- Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascadeP Li
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75235, USA
Cell 91:479-89. 1997....
- I-TASSER server for protein 3D structure predictionYang Zhang
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
BMC Bioinformatics 9:40. 2008..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...
- Data growth and its impact on the SCOP database: new developmentsAntonina Andreeva
MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
Nucleic Acids Res 36:D419-25. 2008The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships...
- HADDOCK: a protein-protein docking approach based on biochemical or biophysical informationCyril Dominguez
Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands
J Am Chem Soc 125:1731-7. 2003..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)...
- Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per proteinYasushi Ishihama
Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
Mol Cell Proteomics 4:1265-72. 2005..This was also the case for 46 proteins in a mouse whole cell lysate...
- Substrate and functional diversity of lysine acetylation revealed by a proteomics surveySung Chan Kim
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Mol Cell 23:607-18. 2006Acetylation 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 for mass spectrometric characterization of proteins and proteomesAndrej Shevchenko
Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
Nat Protoc 1:2856-60. 2006In-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...
- Adapting proteostasis for disease interventionWilliam E Balch
Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Science 319:916-9. 2008....
- Associating genes and protein complexes with disease via network propagationOron Vanunu
School of Computer Science, Tel Aviv University, Tel Aviv, Israel
PLoS Comput Biol 6:e1000641. 2010..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 ..
- Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acidsYasemin Sancak
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Cell 141:290-303. 2010..We show that amino acids induce the movement of mTORC1 to lysosomal membranes, where the Rag proteins reside...
- The FoldX web server: an online force fieldJoost Schymkowitz
Switch Laboratory, Flanders Interuniversity Institute for Biotechnology VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
Nucleic Acids Res 33:W382-8. 2005..that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids...
- Protein homology detection by HMM-HMM comparisonJohannes Söding
Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
Bioinformatics 21:951-60. 2005..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
- Atomic-level characterization of the structural dynamics of proteinsDavid E Shaw
D E Shaw Research, 120 West 45th Street, New York, NY 10036, USA
Science 330:341-6. 2010....
- PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylationPeter V Hornbeck
Cell Signaling Technology, Beverly, MA 01915, USA
Proteomics 4:1551-61. 2004....
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006..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...
- Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensionsE Krissinel
European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, England
Acta Crystallogr D Biol Crystallogr 60:2256-68. 2004..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...
- Extending CATH: increasing coverage of the protein structure universe and linking structure with functionAlison L Cuff
Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
Nucleic Acids Res 39:D420-6. 2011..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 ..
- Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networksTao Huang
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
PLoS ONE 5:e10972. 2010The 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: 2004 updateLukasz Salwinski
Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, 90095-1570, USA
Nucleic Acids Res 32:D449-51. 2004The 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...
- The COG database: an updated version includes eukaryotesRoman L Tatusov
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
BMC Bioinformatics 4:41. 2003..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...
- STITCH 2: an interaction network database for small molecules and proteinsMichael Kuhn
Biotechnology Center, TU Dresden, 01062 Dresden, Germany
Nucleic Acids Res 38:D552-6. 2010Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing...
- Development and testing of a general amber force fieldJunmei Wang
Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
J Comput Chem 25:1157-74. 2004..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, ..
- Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulationsAlexander D MacKerell
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
J Comput Chem 25:1400-15. 2004Computational 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...
- BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinitiesTiqing Liu
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D198-201. 2007..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 ..
- The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamiliesAlison L Cuff
Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
Nucleic Acids Res 37:D310-4. 2009..Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website...
- PRODRG: a tool for high-throughput crystallography of protein-ligand complexesAlexander W Schuttelkopf
Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...
- The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1Yasemin Sancak
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology MIT, Nine Cambridge Center, Cambridge, MA 02142, USA
Science 320:1496-501. 2008..We find that the Rag proteins--a family of four related small guanosine triphosphatases (GTPases)--interact with mTORC1 in an amino acid-..
- A semiempirical free energy force field with charge-based desolvationRuth Huey
Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92102, USA
J Comput Chem 28:1145-52. 2007..The force field shows improvement in redocking simulations over the previous AutoDock3 force field...
- Allosteric regulation and catalysis emerge via a common routeNina M Goodey
Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
Nat Chem Biol 4:474-82. 2008..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 ..
- Quantitative mass spectrometry in proteomics: a critical reviewMarcus Bantscheff
Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
Anal Bioanal Chem 389:1017-31. 2007..These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic ..
- Global dynamics of proteins: bridging between structure and functionIvet Bahar
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
Annu Rev Biophys 39:23-42. 2010..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 ..
- PepX: a structural database of non-redundant protein-peptide complexesPeter Vanhee
VIB Switch Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Nucleic Acids Res 38:D545-51. 2010..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...
- Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factorA Brunet
Children s Hospital and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
Cell 96:857-68. 1999..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...
- Benchmarking sets for molecular dockingNiu Huang
Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143-2550, USA
J Med Chem 49:6789-801. 2006..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
- Tissue specificity and the human protein interaction networkAlice Bossi
EMBL CRG Systems Biology Unit, Centre for Genomic Regulation, UPF, Barcelona, Spain
Mol Syst Biol 5:260. 2009A 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...
- Evolution of biomolecular networks: lessons from metabolic and protein interactionsTakuji Yamada
European Molecular Biology Laboratory, Heidelberg, Germany
Nat Rev Mol Cell Biol 10:791-803. 2009..The nodes of these networks are usually proteins (specifically enzymes in metabolic networks), whereas the links (or edges) are their interactions with other ..
- Protein-protein docking with backbone flexibilityChu Wang
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
J Mol Biol 373:503-19. 2007..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...
- Hunting for "key residues" in the modeling of globular protein folding: an artificial neural network-based approachRoberto Sacile
Department of Communication, Computer and System Sciences DIST, University of Genoa, Via Opera Pia 13, 16145 Genoa, Italy
IEEE Trans Nanobioscience 1:85-91. 2002..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 ..
- FAMS and FAMSBASE for protein structureHideaki Umeyama
Kitasato University, Tokyo, Japan
Curr Protoc Bioinformatics . 2004..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...
- SAD--a normalized structural alignment database: improving sequence-structure alignmentsBrian Marsden
The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Bioinformatics 20:2333-44. 2004..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...
- Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potentialZhijie Liu
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
J Am Chem Soc 126:8515-28. 2004..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...
- Striped sheets and protein contact predictionRobert M MacCallum
Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
Bioinformatics 20:i224-31. 2004Current approaches to contact map prediction in proteins have focused on amino acid conservation and patterns of mutation at sequentially distant positions...
- Probabilistic description of protein alignments for sequences and structuresRyotaro Koike
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
Proteins 56:157-66. 2004A 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 ..
- Designing specificity of protein-substrate interactionsIvan Coluzza
FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
Phys Rev E Stat Nonlin Soft Matter Phys 70:051917. 2004..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...
- Natively disordered proteins: functions and predictionsPedro Romero
Center for Computational Biology and Bioinformatics, Indiana University Purdue University Indianapolis, 714 North Senate Avenue, Indianapolis, IN 46202, USA
Appl Bioinformatics 3:105-13. 2004b>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 to native conformation of a bond-fluctuating protein chain with hydrophobic and polar nodesJohan Bjursell
George Mason University, MS 5C3, Fairfax, Virginia 22030-4444, USA
Phys Rev E Stat Nonlin Soft Matter Phys 70:052904. 2004..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 ...
- SAXS study of the PIR domain from the Grb14 molecular adaptor: a natively unfolded protein with a transient structure primer?K Moncoq
Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculte de Pharmacie, Universite Paris 5, 75270 Paris Cedex 06, France
Biophys J 87:4056-64. 2004..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...
- Tertiary structure predictions on a comprehensive benchmark of medium to large size proteinsYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 87:2647-55. 2004We 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-..
- NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharidesNuria Aboitiz
Department of Protein Structure and Function, , CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
Chembiochem 5:1245-55. 2004..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...
- Interaction between the internal motif KTXXXI of Idax and mDvl PDZ domainTimothy B C London
Department of Structural Biology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
Biochem Biophys Res Commun 322:326-32. 2004..Such internal motif identified in this study suggests a new type of sequence motif recognition for Dvl PDZ domain...
- Five hierarchical levels of sequence-structure correlation in proteinsChristopher Bystroff
Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
Appl Bioinformatics 3:97-104. 2004..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 protein coarse contact mapsAlessandro Vullo
Department of Systems and Computer Science, Universita di Firenze, Via di Santa Marta 3, I 50139 Firenze Italy
J Bioinform Comput Biol 1:411-31. 2003Prediction of topological representations of proteins that are geometrically invariants can contribute towards the solution of fundamental open problems in structural genomics like folding...
- Protein structure alignment and fast similarity search using local shape signaturesTolga Can
Department of Computer Science, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
J Bioinform Comput Biol 2:215-39. 2004..We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful...
- Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource dataWerner G Krebs
Department of Pharmacology, Integrative Biosciences, San Diego Supercomputer Center Dept 0505, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
J Bioinform Comput Biol 2:61-75. 2004..g., ligand binding) and mutations. The PMR morph movies and statistics can be freely viewed from the PMR website, http://pmr.sdsc.edu...
- STRUCTURE, BIOSYNTHESIS AND FUNCTION OF GLYCOPROTEINSStuart Kornfeld; Fiscal Year: 2007..GST peptides with these amino acids will be used to isolate proteins that recognize these motifs...
- MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SABuddy Ullman; Fiscal Year: 2003..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
- Apoptosis and Trophoblast FusionNEAL STEWART ROTE; Fiscal Year: 2010..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...
- Apoptosis and Trophoblast FusionNeal Rote; Fiscal Year: 2009..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...
- ADIPOCYTE PROTEIN SECRETION AND INSULIN ACTIONHarvey Lodish; Fiscal Year: 2007..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 ..
- Ty3 viruslike particle morphogenesis and host interactionsSuzanne Sandmeyer; Fiscal Year: 2010..terminal repeat retrotransposon in budding yeast containing GAG3 and POL3 ORFs encoding structural and catalytic proteins, respectively...
- A novel transgenic silkworm system for recombinant glycoprotein productionDonald Jarvis; Fiscal Year: 2009Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
- A novel transgenic silkworm system for recombinant glycoprotein productionDonald L Jarvis; Fiscal Year: 2010Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
- A novel transgenic silkworm system for recombinant glycoprotein productionDonald Jarvis; Fiscal Year: 2007Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
- CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGSSTEPHEN LIPPARD; Fiscal Year: 2007..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...
- CELL CYCLE REGULATION OF THE YEAST HO GENELINDA BREEDEN; Fiscal Year: 2001..Most of the research proposal is an investigation of the proteins and protein binding sites required for these two waves of transcriptional activation...
- NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINSFrances Walker; Fiscal Year: 2009..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas' disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...
- NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINSFrances Walker; Fiscal Year: 2009..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 epitope recognition by CD8+ T cellsJEROME SCOTT HARMS; Fiscal Year: 2010Brucella 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 epitope recognition by CD8+ T cellsGary Splitter; Fiscal Year: 2009Brucella 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...
- Genetic control of limb development by PbxLicia Selleri; Fiscal Year: 2010..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"...
- NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINSFrances Walker; Fiscal Year: 2006We 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...
- NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINSFRANCES ANN WALKER; Fiscal Year: 2010..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas'disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...
- Vaccinia Virus Genetics and MorphogenesisRichard C Condit; Fiscal Year: 2010..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 ..
- Investigation of protein interactions in intrinsic blood coagulation pathwayDivi Venkateswarlu; Fiscal Year: 2007..During the requested funding period, we propose to develop structural assembly of multi-domain proteins associated with intrinsic blood coagulation pathway...