research library browse by date
The collection includes articles from PSI research groups and the broader community
January 2009
Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses
Zhang P., Mueller S., Morais M., Bator C., Bowman V. et al.
Proc Natl Acad Sci USA 105, 18284 - 18289 (2008)
Structural basis of sequence-specific collagen recognition by SPARC
Hohenester E., Sasaki T., Giudici C., Farndale R. and Bächinger H.
Proc Natl Acad Sci USA 105, 18273 - 18277 (2008)
Structure of macrophage colony stimulating factor bound to FMS: Diverse signaling assemblies of class III receptor tyrosine kinases
Chen X., Liu H., Focia P., Shim A. and He X.
Proc Natl Acad Sci USA 105, 18267 - 18272 (2008)
A structural and biochemical basis for PAPS-independent sulfuryl transfer by aryl sulfotransferase from uropathogenic Escherichia coli
Malojcic G., Owen R., Grimshaw J., Brozzo M., Dreher-Teo H. et al.
Proc Natl Acad Sci USA 105, 19217 - 19222 (2008)
Structural consequences of effector protein complex formation in a diiron hydroxylase
Bailey L., McCoy J., Phillips J.G. and Fox B.
Proc Natl Acad Sci USA 105, 19194 - 19198 (2008)
Detection of functionally important regions in "hypothetical proteins" of known structure
Nimrod G., Schushanm M., Steinberg D. and Ben-Tal N.
Structure 16, 1755 - 1763 (2008)
The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist
Jaakola V., Griffith M., Hanson M., Cherezov V., Chien E. et al.
Science 322, 1211 - 1217 (2008)
Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats
Brohawn S., Leksa N., Spear E., Rajashankar K. and Schwartz T.
Science 322, 1369 - 1373 (2008)
Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation
Gsponer J., Futschik M., Teichmann S. and Babu M.
Science 322, 1365 - 1368 (2008)
Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin
Hanna R., Campbell R. and Davies P.
Nature 456, 409 - 412 (2008)
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains
Moldoveanu T., Gehring K. and Green D.
Nature 456, 404 - 408 (2008)
Structure of the intact PPAR-[ggr]-RXR-[agr] nuclear receptor complex on DNA
Chandra V., Huang P., Hamuro Y., Raghuram S., Wang Y. et al.
Nature 456, 350 - 356 (2008)
Structural basis for gibberellin recognition by its receptor GID1
Shimada A., Ueguchi-Tanaka M., Nakatsu T., Nakajima M., Naoe Y. et al.
Nature 456, 520 - 523 (2008)
Gibberellin-induced DELLA recognition by the gibberellin receptor GID1
Murase K., Hirano Y., Sun T. and Hakoshima T.
Nature 456, 459 - 463 (2008)
Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats
Monne M., Han L., Schwend T., Burendahl S. and Jovine L.
Nature 456, 653 - 657 (2008)
Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin
Byres E., Paton A., Paton J., Lofling J., Smith D. et al.
Nature 456, 648 - 652 (2008)
Fertilization: Welcome to the fold
Wassarman P.
Nature 456, 586 - 587 (2008)
Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.
Singer A., Rohde J., Lam R., Skarina T., Kagan O. et al.
Nat Struct Mol Biol 15, 1293 - 1301 (2008)
Toward chaperone-assisted crystallography: Protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold
Tereshko V., Uysal S., Koide A., Margalef K., Koide S. et al.
Protein Sci 17, 1175 - 1187 (2008)
Genomic-scale prioritization of drug targets: the TDR Targets database
Agüero F., Al-Lazikani B., Aslett M., Berriman M., Buckner F. et al.
Nature Rev Drug Discov 7, 900 - 907 (2008)
Allochromatium vinosum DsrC: Solution-State NMR Structure, Redox Properties, and Interaction with DsrEFH, a Protein Essential for Purple Sulfur Bacterial Sulfur Oxidation
Cort J., Selan U., Schulte A., Grimm F., Kennedy M. et al.
J Mol Biol 382, 692 - 707 (2008)
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
Wilson C., Kreychman J. and Gerstein M.
J Mol Biol 297, 233 - 249 (2000)
Electrostatic aspects of protein-protein interactions.
Sheinerman F., Norel R. and Honig B.
Curr Opin Struct Biol 10, 153 - 159 (2000)
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
Lin J. and Gerstein M.
Genome Res 10, 808 - 818 (2000)
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
Drawid A. and Gerstein M.
J Mol Biol 301, 1059 - 1075 (2000)
The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
Gerstein M. and Jansen R.
Curr Opin Struct Biol 10, 574 - 584 (2000)
Structural proteomics: prospects for high throughput sample preparation
Christendat D., Yee A., Dharamsi A., Kluger Y., Gerstein M. et al.
Prog Biophys Mol Biol 73, 339 - 345 (2000)
Protein production: feeding the crystallographers and NMR spectroscopists
Edwards A., Arrowsmith C., Christendat D., Dharamsi A., Friesen J. et al.
Nature Struct Biol 7, 970 - 972 (2000)
Protein NMR spectroscopy in structural genomics
Montelione G., Zheng D., Huang Y., Gunsalus K. and Szyperski T.
Nat Struct Biol 7 Suppl, 982 - 985 (2000)
Synchrotron crystallography.
Hendrickson W.
Trends Biochem Sci 25, 637 - 643 (2000)
Comparing function and structure between entire proteomes.
Liu J. and Rost B.
Protein Sci 10, 1970 - 1979 (2001)
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
Hegyi H. and Gerstein M.
Genome Res 11, 1632 - 1640 (2001)
A snapshot of Nature's favorite pump
Thomas P. and Hunt J.
Nature Struct Biol 8, 920 - 923 (2001)
Structural genomics: an approach to the protein folding problem
Montelione G.
Proc Natl Acad Sci USA 98, 13488 - 13489 (2001)
Continuum secondary structure captures protein flexibility
Andersen C., Palmer A., Brunak S. and Rost B.
Structure 10, 175 - 184 (2002)
Structural genomics: a new era for pharmaceutical research
Liu Y., Luscombe N., Alexandrov V., Bertone P., Harrison P. et al.
Genome Biol 3, (2002)
Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds
Hegyi H., Lin J., Greenbaum D. and Gerstein M.
Proteins 47, 126 - 141 (2002)
A protein sequence that can encode native structure by disfavoring alternate conformations.
Wigley W., Corboy M., Cutler T., Thibodeau P., Oldan J. et al.
Nature Struct Biol 9, 381 - 388 (2002)
Enzyme function less conserved than anticipated
Rost B.
J Mol Biol 318, 595 - 608 (2002)
Did evolution leap to create the protein universe?
Rost B.
Curr Opin Struct Biol 12, 409 - 416 (2002)
Loopy proteins appear conserved in evolution
Liu J., Tan H. and Rost B.
J Mol Biol 322, 53 - 64 (2002)
Bridging structural biology and genomics: assessing protein interaction data with known complexes
Edwards A., Kus B., Jansen R., Greenbaum D., Greenblatt J. et al.
Trends Genet 18, 529 - 536 (2002)
Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes
Zhang Z., Harrison P. and Gerstein M.
J Mol Biol 323, 811 - 822 (2002)
Understanding biology through intelligent systems
Jurisica I. and Wigle D.
Genome Biol 3, (2002)
Long membrane helices and short loops predicted less accurately
Chen C. and Rost B.
Protein Sci 11, 2766 - 2773 (2002)
Transmembrane helix predictions revisited
Chen C., Kernytsky A. and Rost B.
Protein Sci 11, 2774 - 2791 (2002)
Sequence conserved for subcellular localization
Nair R. and Rost B.
Protein Sci 11, 2836 - 2847 (2002)
Analysing six types of protein-protein interfaces
Ofran Y. and Rost B.
J Mol Biol 325, 377 - 387 (2003)
NLSdb: database of nuclear localization signals
Nair R., Carter P. and Rost B.
Nucleic Acids Res 31, 397 - 399 (2003)
PEP: Predictions for entire proteomes
Carter P., Liu J. and Rost B.
Nucleic Acids Res 31, 410 - 413 (2003)
Domains, motifs and clusters in the protein universe
Liu J. and Rost B.
Curr Opin Chem Biol 7, 5 - 11 (2003)
Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level
Lan N., Montelione G. and Gerstein M.
Curr Opin Chemical Biol 7, 44 - 54 (2003)
Structural genomics: current progress
Gerstein M., Edwards A., Arrowsmith C. and Montelione G.
Science 299, (2003)
Predicted protein-protein interaction sites from local sequence information
Ofran Y. and Rost B.
FEBS Lett 544, 236 - 239 (2003)
DSSPcont: Continuous secondary structure assignments for proteins
Carter P., Andersen C. and Rost B.
Nucleic Acids Res 31, 3293 - 3295 (2003)
META-PP: single interface to crucial prediction servers
Eyrich V. and Rost B.
Nucleic Acids Res 31, 3308 - 3310 (2003)
NORSp: Predictions of long regions without regular secondary structure
Liu J. and Rost B.
Nucleic Acids Res 31, 3833 - 3835 (2003)
Structural genomics in pharmaceutical design
Mueller L. and Montelione G.
J Struct Funct Genomics 2, 67 - 70 (2002)
Integration of genomic datasets to predict protein complexes in yeast
Jansen R., Lan N., Qian J. and Gerstein M.
J Struct Funct Genomics 2, 71 - 81 (2002)
Structural genomics: Computational methods for structure analysis
Goldsmith-Fischman S. and Honig B.
Protein Sci 12, 1813 - 1821 (2003)
Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains
Singh S. and Murray D.
Protein Sci 12, 1934 - 1953 (2003)
A Bayesian networks approach for predicting protein-protein interactions from genomic data
Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N. et al.
Science 302, 449 - 453 (2003)
Automatic prediction of protein function.
Rost B., Liu J., Nair R., Wrzeszczynski K. and Ofran Y.
Cell Mol Life Sci 60, 2637 - 2650 (2003)
Exploring the range of protein flexibility, from a structural proteomics perspective
Gerstein M. and Echols N.
Curr Opin Chem Biol 8, 14 - 19 (2004)
Conformational changes associated with protein-protein interactions
Goh C., Milburn D. and Gerstein M.
Curr Opin Struct Biol 14, 104 - 109 (2004)
CHOP proteins into structural domain-like fragments
Liu J. and Rost B.
Proteins 55, 678 - 688 (2004)
Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes.
Wrzeszczynski K. and Rost B.
Cell Mol Life Sci 61, 1341 - 1353 (2004)
Analyzing cellular biochemistry in terms of molecular networks.
Annu Rev Biochem 73, 1051 - 1087 (2004)
[doi: http://dx.doi.org/10.1146/annurev.biochem.73.011303.073950]
Sequence-based prediction of protein domains
Liu J. and Rost B.
Nucleic Acids Res 32, 3522 - 3530 (2004)
Improving fold recognition without folds
Przybylski D. and Rost B.
J Mol Biol 341, 255 - 269 (2004)
PubNet: a flexible system for visualizing literature derived networks
Douglas S., Montelione G. and Gerstein M.
Genome Biol 6, (2005)
Structural biology: proteins flex to function
Huang Y. and Montelione G.
Nature 438, 36 - 37 (2005)
Comparing classical pathways and modern networks: towards the development of an edge ontology.
Lu L., Sboner A., Huang Y., Lu H., Gianoulis T. et al.
Trends Biochem Sci 32, 320 - 331 (2007)
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing
Andrec M., Snyder D., Zhou Z., Young J., Montelione G. et al.
Proteins 69, 449 - 465 (2007)
Natively unstructured loops differ from other loops
PLoS Comp Biol 3, (2007)
Structural and functional studies of the abundant tegument protein ORF52 from murine gammaherpesvirus 68
Benach J., Wang L., Chen Y., Ho C., Lee S. et al.
J Biol Chem 282, 31534 - 31541 (2007)
X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus.
Madegowda M., Eswaramoorthy S., Burley S. and Swaminathan S.
Proteins 71, 534 - 540 (2008)
NMR structure of protein Cgl2762 from Corynebacterium glutamicum implicated in DNA transposition reveals a helix-turn-helix motif attached to a flexibly disordered leucine zipper
Singarapu K., Xiao R., Sukumaran D., Acton T., Montelione G. et al.
Proteins 70, 1650 - 1654 (2008)
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain
Wu B., Yee A., Huang Y., Ramelot T., Cort J. et al.
Protein Sci 17, 583 - 588 (2008)
NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors
Singarapu K., Xiao R., Acton T., Rost B., Montelione G. et al.
Proteins 71, 1027 - 1031 (2008)
Molecular insights into the biosynthesis of the F420 coenzyme
Forouhar F., Abashidze M., Xu H., Grochowski L., Seetharaman J. et al.
J Biol Chem 283, 11832 - 11840 (2008)
Effect of low-complexity regions on protein structure determination.
Bannen R., Bingman C. and Phillips J.G.
J Struct Funct Genomics 8, 217 - 226 (2007)
Consistent blind protein structure generation from NMR chemical shift data
Shen Y., Lange O., Delaglio F., Rossi P., Aramini J. et al.
Proc Natl Acad Sci USA 105, 4685 - 4690 (2008)
Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis
Aramini J., Sharma S., Huang Y., Swapna G., Ho C. et al.
Proteins 72, 526 - 530 (2008)
Targeting the human cancer pathway protein interaction network by structural genomics.
Huang Y., Hang D., Lu L., Tong L., Gerstein M. et al.
Mol Cell Proteomics 7, 2048 - 2060 (2008)
Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae
Ragumani S., Kumaran D., Burley S. and Swaminathan S.
Proteins 72, 1096 - 1103 (2008)
Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum.
Newby Z., O'Connell J., Robles-Colmenares Y., Khademi S., Miercke L. et al.
Nature Struct Mol Biol 15, 619 - 625 (2008)
Metallomics and metalloproteomics.
Shi W. and Chance M.
Cell Mol Life Sci 65, 3040 - 3048 (2008)
Structural characterization and reversal of the natural organophosphate resistance of a D-type esterase, Saccharomyces cerevisiae S-formylglutathione hydrolase
Legler P., Kumaran D., Swaminathan S., Studier F. and Millard C.
Biochemistry 47, 9592 - 9601 (2008)
Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad
Aramini J., Rossi P., Huang Y., Zhao L., Jiang M. et al.
Biochemistry 47, 9715 - 9717 (2008)
Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding
Thackray S., Bruckmann C., Anderson J., Campbell L., Xiao R. et al.
Biochemistry 47, 10677 - 10684 (2008)
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation
Vila J., Aramini J., Rossi P., Kuzin A., Su M. et al.
Proc Natl Acad Sci USA 105, 14389 - 14394 (2008)
How well can the accuracy of comparative protein structure models be predicted?
Eramian D., Eswar N., Shen M. and Sali A.
Protein Sci 17, 1881 - 1893 (2008)
Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites.
Binkowski T. and Joachimiak A.
BMC Struct Biol 8, (2008)
Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis.
Pfleger B., Kim Y., Nusca T., Maltseva N., Lee J. et al.
Proc Natl Acad Sci USA 105, 17133 - 17138 (2008)
A Family of LIC Vectors for High-Throughput Cloning and Purification of Proteins
Eschenfeldt W., Lucy S., Millard C., Joachimiak A. and Mark I.
Meth Mol Biol 498, 105 - 115 (2009)
"System 48" high-throughput cloning and protein expression analysis.
Abdullah J., Joachimiak A. and Collart F.
Meth Mol Biol 498, 117 - 127 (2009)
Genome pool strategy for structural coverage of protein families
Jaroszewski L., Slabinski L., Wooley J., Deacon A., Lesley S. et al.
Structure 16, 1659 - 1667 (2008)
Structure of the guide-strand-containing argonaute silencing complex
Wang Y., Sheng G., Juranek S., Tuschl T. and Patel D.
Nature 456, 209 - 213 (2008)
Structural basis for RNA recognition by a type II poly(A)-binding protein.
Song J., McGivern J., Nichols K., Markley J. and Sheets M.
Proc Natl Acad Sci 105, 15317 - 15322 (2008)
