Search Results - "Freer, S T"

Deciphering common failures in molecular docking of ligand-protein complexes by Verkhivker, G M, Bouzida, D, Gehlhaar, D K, Rejto, P A, Arthurs, S, Colson, A B, Freer, S T, Larson, V, Luty, B A, Marrone, T, Rose, P W

“…Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligand-protein systems by a combined thermodynamic and…”
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De Novo Design of Enzyme Inhibitors by Monte Carlo Ligand Generation by Gehlhaar, Daniel K, Moerder, Karl E, Zichi, Dominic, Sherman, Christopher J, Ogden, Richard C, Freer, Stephan T

“…A new computational method for the in situ generation of small molecules within the binding site of a protein is described. The method has been evaluated using…”
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Crystal structure of avian dihydrofolate reductase containing phenyltriazine and NADPH by Volz, K W, Matthews, D A, Alden, R A, Freer, S T, Hansch, C, Kaufman, B T, Kraut, J

“…The structure of chicken liver dihydrofolate reductase (5,6,7,8-tetrahydrofolate: NADP super(+) oxidoreductase (EC 1.5.1.3)), in a ternary complex with NADPH…”
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X-ray crystallographic study of boronic acid adducts with subtilisin BPN' (Novo). A model for the catalytic transition state by Matthews, D A, Alden, R A, Birktoft, J J, Freer, S T, Kraut, J

“…We have studied the structures of adducts formed between subtilisin BPN' and both benzeneboronic acid and 2-phenylethaneboronic acid by x-ray diffraction…”
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Dihydrofolate reductase from Lactobacillus casei. Stereochemistry of NADPH binding by Matthews, D A, Alden, R A, Freer, S T, Xuong, N, Kraut, J

“…The NADPH molecule binds to dihydrofolate reductase in an extended conformation. Several of the individual dihedral angles, especially in the adenine…”
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The crystal structure of [yeast] cytochrome c peroxidase by Poulos, T.L, Freer, S.T, Alden, R.A, Edwards, S.L, Skogland, U, Takio, K, Eriksson, B, Xuong, N, Yonetani, T, Kraut, J

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Dihydrofolate Reductase: X-ray Structure of the Binary Complex with Methotrexate by Matthews, D. A., Alden, R. A., Bolin, J. T., Freer, S. T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M., Hoogsteen, K.

“…A central eight-stranded β-pleated sheet is the main feature of the polypeptide backbone folding in dihydrofolate reductase. The innermost four strands and two…”
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Crystallographic structure refinement of Chromatium high potential iron protein at two Angstroms resolution by S T Freer, R A Alden, C W Carter, Jr, J Kraut

“…The structure of Chromatium high potential iron protein (HiPIP) has been refined by semiautomatic Fo-Fc (observed minus calculated structure amplitude Fourier…”
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Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes by Verkhivker, G M, Rejto, P A, Gehlhaar, D K, Freer, S T

“…Energy landscapes of molecular recognition are explored by performing "semi-rigid" docking of FK-506 and rapamycin with the Fukisawa binding protein (FKBP-12),…”
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Design of thymidylate synthase inhibitors using protein crystal structures: the synthesis and biological evaluation of a novel class of 5-substituted quinazolinones by Webber, Stephen E, Bleckman, Ted M, Attard, John, Deal, Judith G, Kathardekar, Vinit, Welsh, Katherine M, Webber, Stephanie, Janson, Cheryl A, Matthews, David A

“…The design, synthesis, and biological evaluation of a new class of inhibitors of thymidylate synthase (TS) is described. The molecular design was carried out…”
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The Structure of Oxidized Cytochrome c2 of Rhodospirillum rubrum by Salemme, F.R., Freer, S.T., Xuong, Ng. H., Alden, R.A., Kraut, J.

“…The structure of ferricytochrome c 2 from the non-sulfur purple photosynthetic bacterium Rhodospirillum rubrum has been determined at 2 A resolution by x-ray…”
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A Comparison of Fe4S4 Clusters in High-Potential Iron Protein and in Ferredoxin by Carter, C. W., Kraut, J., Freer, S. T., Alden, R. A., Sieker, L. C., Adman, E., Jensen, L. H.

“…The structures of both oxidized (HPox) and reduced (HPred) high-potential iron protein and of oxidized ferredoxin (Fdox) have been partially refined at 2.0-…”
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Protein conformational substates from X-ray crystallography by Rejto, Paul A., Freer, Stephan T.

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Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains by Verkhivker, Gennady M., Bouzida, Djamal, Gehlhaar, Daniel K., Rejto, Paul A., Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…Computer simulations using the simplified energy function and simulated tempering dynamics have accurately determined the native structure of the pYVPML,…”
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Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides by Verkhivker, Gennady M, Bouzida, Djamal, Gehlhaar, Daniel K, Rejto, Paul A, Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B, Freer, Stephan T, Larson, Veda, Luty, Brock A, Marrone, Tami, Rose, Peter W

“…Structure and energetics of the Src Src Homology 2 (SH2) domain binding with the recognition phosphopeptide pYEEI and its mutants are studied by a hierarchical…”
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Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions by Verkhivker, Gennady M., Rejto, Paul A., Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)–dihydrofolate reductase (DHFR) ligand–protein system are investigated…”
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Crystallographic determination of the heme orientation and location of the cyanide binding site in yeast cytochrome c peroxidase by Poulos, T.L., Freer, S.T., Alden, R.A., Xuong, N.H., Edwards, S.L., Hamlin, R.C., Kraut, J.

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Polypeptide halomethyl ketones bind to serine proteases as analogs of the tetrahedral intermediate. X-ray crystallographic comparison of lysine- and phenylalanine-polypeptide chloromethyl ketone-inhibited subtilisin by Poulos, T L, Alden, R A, Freer, S T, Birktoft, J J, Kraut, J

“…1. A detailed study of cytochrome C oxidse activity with Keilin-Hartree particles and purified beef heart enzyme, at low ionic strength and low cytochrome C…”
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Design of enzyme inhibitors using iterative protein crystallographic analysis by Appelt, Krzysztof, Bacquet, Russell J, Bartlett, Charlotte A, Booth, Carol L. J, Freer, Stephan T, Fuhry, Mary Ann M, Gehring, Michael R, Herrmann, Steven M, Howland, Eleanor F

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An analysis of the sedimentation coefficient distribution of a sample of calf thymus DNA by Schumaker, V N, Richards, E G, Freer, S T

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