Search Results - "Deane, C. M."

Reduced amounts and abnormal forms of phospholipase C zeta (PLCζ) in spermatozoa from infertile men by Heytens, E., Parrington, J., Coward, K., Young, C., Lambrecht, S., Yoon, S.-Y., Fissore, R.A., Hamer, R., Deane, C.M., Ruas, M., Grasa, P., Soleimani, R., Cuvelier, C.A., Gerris, J., Dhont, M., Deforce, D., Leybaert, L., De Sutter, P.

“…BACKGROUND In mammals, oocyte activation at fertilization is thought to be induced by the sperm-specific phospholipase C zeta (PLCζ). However, it still remains…”
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HOMSTRAD: A database of protein structure alignments for homologous families by Mizuguchi, Kenji, Deane, Charlotte M., Blundell, Tom L., Overington, John P.

“…We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned…”
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ABangle: characterising the VH–VL orientation in antibodies by Dunbar, J., Fuchs, A., Shi, J., Deane, C.M.

“…The binding site of an antibody is formed between the two variable domains, VH and VL, of its antigen binding fragment (Fab). Understanding how VH and VL…”
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JOY: protein sequence-structure representation and analysis by Mizuguchi, K, Deane, C.M, Blundell, T.L, Johnson, M.S, Overington, J.P

“…JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information…”
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Antibody H3 Structure Prediction by Marks, C., Deane, C.M.

“…Antibodies are proteins of the immune system that are able to bind to a huge variety of different substances, making them attractive candidates for therapeutic…”
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Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking by Krawczyk, Konrad, Baker, Terry, Shi, Jiye, Deane, Charlotte M.

“…Antibodies are a class of proteins indispensable for the vertebrate immune system. The general architecture of all antibodies is very similar, but they contain…”
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A maternally inherited autosomal point mutation in human phospholipase C zeta (PLCζ) leads to male infertility by Kashir, Junaid, Konstantinidis, Michalis, Jones, Celine, Lemmon, Bernadette, Chang Lee, Hoi, Hamer, Rebecca, Heindryckx, Bjorn, Deane, Charlotte M., De Sutter, Petra, Fissore, Rafael A., Parrington, John, Wells, Dagan, Coward, Kevin

“…BACKGROUND Male factor and idiopathic infertility contribute significantly to global infertility, with abnormal testicular gene expression considered to be a…”
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CommWalker: correctly evaluating modules in molecular networks in light of annotation bias by Luecken, M D, Page, M J T, Crosby, A J, Mason, S, Reinert, G, Deane, C M

“…Abstract Motivation Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard…”
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WONKA: objective novel complex analysis for ensembles of protein–ligand structures by Bradley, A. R., Wall, I. D., von Delft, F., Green, D. V. S., Deane, C. M., Marsden, B. D.

“…WONKA is a tool for the systematic analysis of an ensemble of protein–ligand structures. It makes the identification of conserved and unusual features within…”
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Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure by Burke, David F., Deane, Charlotte M., Blundell, Tom L.

“…We describe a web server, which provides easy access to the SLoop database of loop conformations connecting elements of protein secondary structure. The loops…”
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Sequence-structure homology recognition by iterative alignment refinement and comparative modeling by Williams, M.G., Shirai, H., Shi, J., Nagendra, H.G., Mueller, J., Mizuguchi, K., Miguel, R.N., S.C. Lovell, Innis, C.A., Deane, C.M., Chen, L., Campillo, N., Burke, D.F., Blundell, T.L., de Bakker, P.I.W.

“…Our approach to fold recognition for the fourth critical assessment of techniques for protein structure prediction (CASP4) experiment involved the use of the…”
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CODA: A combined algorithm for predicting the structurally variable regions of protein models by Deane, Charlotte M., Blundell, Tom L.

“…CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab…”
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How old is your fold? by Winstanley, Henry F., Abeln, Sanne, Deane, Charlotte M.

“…Motivation: At present there exists no age estimate for the different protein structures found in nature. It has become clear from occurrence studies that…”
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Improved protein loop prediction from sequence alone by Burke, David F., Deane, Charlotte M.

“…The SLoop database of supersecondary fragments, first described by Donate et al. (Protein Sci., 1996, 5, 2600–2616), contains protein loops, classified…”
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A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins by Deane, Charlotte M., Blundell, Tom L.

“…We present a fast ab initio method for the prediction of local conformations in proteins. The program, PETRA, selects polypeptide fragments from a…”
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The Role and Predicted Propensity of Conserved Proline Residues in the 5-HT3 Receptor by Deane, Charlotte M., Lummis, Sarah C.R.

“…5-HT3 receptors possess a number of highly conserved proline residues. We changed each of these to alanine, expressed the mutants as homomeric 5-HT3Areceptors…”
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Carbonyl–carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid by Deane, Charlotte M., Allen, Frank H., Taylor, Robin, Blundell, Tom L.

“…Asparagine and aspartate are known to adopt conformations in the left-handed α-helical region and other partially allowed regions of the Ramachandran plot more…”
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Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations by Knapp, Bernhard, Demharter, Samuel, Esmaielbeiki, Reyhaneh, Deane, Charlotte M

“…The interaction between T-cell receptors (TCRs) and major histocompatibility complex (MHC)-bound epitopes is one of the most important processes in the…”
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SCORE: predicting the core of protein models by Deane, Charlotte M., Kaas, Quentin, Blundell, Tom L.

“…Motivation: The prediction of the regions of homology models that can be ‘restrained by’ or ‘copied from’ the basis structures is a vital step in correct model…”
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An iterative structure-assisted approach to sequence alignment and comparative modeling by Burke, David F., Deane, Charlotte M., Nagarajaram, Hampapathalu A., Campillo, Nuria, Martin-Martinez, Mercedes, Mendes, Joaquim, Molina, Franck, Perry, Jeff, Reddy, B.V.B., Soares, Claudio M., Steward, Robert E., Williams, Mark, Carrondo, Maria Armenia, Blundell, Tom L., Mizuguchi, Kenji

“…Correct alignment of the sequence of a target protein with those of homologues of known three‐dimensional structure is a key step in comparative modeling…”
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