Genomes and Genes
Peter J Steinbach
Affiliation: National Institutes of Health
- Filtering artifacts from lifetime distributions when maximizing entropy using a bootstrapped modelPeter J Steinbach
Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
Anal Biochem 427:102-5. 2012..despite the presence of increased noise. In a second example, ambiguity in the interpretation of Poisson kinetics in the presence of scattered excitation light is resolved by filtering the prior model...
- Water-exclusion and liquid-structure forces in implicit solvationSergio A Hassan
Center for Molecular Modeling, DCB CIT, National Institutes of Health, US DHHS, Bethesda, Maryland 20892, United States
J Phys Chem B 115:14668-82. 2011..The current implementation is ~1.5 times slower than the gas-phase force field and exhibits good parallel performance...
- Computer simulation of protein-ligand interactions: challenges and applicationsSergio A Hassan
Center for Molecular Modeling, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health DHHS, Bethesda, MD 20892, USA
Methods Mol Biol 305:451-92. 2005..The results of these relatively simple conformational searches underscore the importance of incorporating protein flexibility in simulations of protein-ligand interactions, even in the context of relatively rigid binding pockets...
- Design of drug-resistant alleles of type-III phosphatidylinositol 4-kinases using mutagenesis and molecular modelingAndras Balla
Section on Molecular Signal Transduction, Center for Developmental Neuroscience, NICHD, National Institutes of Health, Bethesda, Maryland 20892 4510, USA
Biochemistry 47:1599-607. 2008..These studies should aid development of subtype-specific inhibitors of type-III PI4Ks and help to better understand the significance of localized PtdIns4P production by the various PI4Ks isoforms in specific cellular compartments...
- Prediction of side-chain conformations on protein surfacesZhexin Xiang
Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 5624, USA
Proteins 66:814-23. 2007..The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 A, with and without consideration of crystal packing effects, respectively...
- Exploring peptide energy landscapes: a test of force fields and implicit solvent modelsPeter J Steinbach
Center for Molecular Modeling, National Institutes of Health, DHHS, Bethesda, Maryland 20892 5624, USA
Proteins 57:665-77. 2004..The thousands of simulations reported here suggest that the prediction of protein structure might be improved by the simultaneous use of a CMAP-like description of the main chain and an EEF1-like description of the solvent...
- Analysis of kinetics using a hybrid maximum-entropy/nonlinear-least-squares method: application to protein foldingPeter J Steinbach
Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
Biophys J 82:2244-55. 2002..Analysis of the folding of dihydrofolate reductase reveals six kinetic processes, one more than previously reported...
- Biological effect of a novel mutation in the third leucine-rich repeat of human luteinizing hormone receptorMichael Yiu Kwong Leung
Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Building 49, Room 2A08, 49 Convent Drive, MSC 4429, Bethesda, Maryland 20892 4429, USA
Mol Endocrinol 20:2493-503. 2006..This mutation might also affect an LHR-dimer interaction. Thus, the I114F mutation reduces ligand binding and signal transduction by the hLHR, and it is partially responsible for Leydig cell hypoplasia in the patient...
- Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescenceBenjamin Schuler
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Building 5, Room 104, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 102:2754-9. 2005....
- Identifying protein kinase target preferences using mass spectrometryJacqueline Douglass
National Institutes of Health, Bethesda, MD 20892 1603, USA
Am J Physiol Cell Physiol 303:C715-27. 2012....
- Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domainSergei A Gaidamakov
Laboratory of Molecular Genetics, National Institute of Child Health and Human Development Bethesda, MD 20892, USA
Nucleic Acids Res 33:2166-75. 2005..In mitochondria, where RNase H1 is essential for DNA formation during embryogenesis, long hybrids may be involved in DNA replication...
- The Tensin-3 protein, including its SH2 domain, is phosphorylated by Src and contributes to tumorigenesis and metastasisXiaolan Qian
Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Cancer Cell 16:246-58. 2009..Thus, tensin-3 is implicated as an oncoprotein regulated by Src and possessing an SH2 domain with a previously undescribed mechanism for the regulation of ligand binding...
- Mutation in the leucine-rich repeat C-flanking region of platelet glycoprotein Ib beta impairs assembly of von Willebrand factor receptorJingrong Tang
Unit on Pediatric Genetics, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
Thromb Haemost 92:75-88. 2004....
- Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallographyRuiai Chu
Laboratory of Biochemistry, Building 37, Room 6114E, National Cancer Institute, NIH, Bethesda, MD 20892 4255, USA
J Mol Biol 323:253-62. 2002..These results suggest that the hydrophobic interactions in the core are not sufficient to dictate the selection and that the location of the cutting site of the protease also influences the selection of structures...