Homology modeling and simulations of nuclease structures.

PubWeight™: 0.98‹?› | Rank: Top 15%

🔗 View Article (PMID 11265289)

Published in Methods Mol Biol on January 01, 2001

Authors

K V Soman1, C H Schein, H Zhu, W Braun

Author Affiliations

1: Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA.

Articles citing this

Selectively receptor-blind measles viruses: Identification of residues necessary for SLAM- or CD46-induced fusion and their localization on a new hemagglutinin structural model. J Virol (2004) 2.42

SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res (2003) 1.61

Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion. J Biol Chem (2012) 1.18

Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry in peripheral blood mononuclear cells. J Virol (2005) 1.17

Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J Mol Model (2006) 1.00

Structure-function analysis of decay-accelerating factor: identification of residues important for binding of the Escherichia coli Dr adhesin and complement regulation. Infect Immun (2002) 0.91

Structural basis for epitope sharing between group 1 allergens of cedar pollen. Mol Immunol (2005) 0.91

A multimeric model for murine anti-apoptotic protein Bcl-2 and structural insights for its regulation by post-translational modification. J Mol Model (2003) 0.86

Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes. Vaccine (2012) 0.79

Complement protective epitopes and CD55-microtubule complexes facilitate the invasion and intracellular persistence of uropathogenic Escherichia coli. J Infect Dis (2013) 0.78

Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. BMC Bioinformatics (2012) 0.77

Modulation of the processive abasic site lyase activity of a pyrimidine dimer glycosylase. DNA Repair (Amst) (2011) 0.76

Articles by these authors

(truncated to the top 100)

Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. Cell (1998) 16.08

Caspase-12 mediates endoplasmic-reticulum-specific apoptosis and cytotoxicity by amyloid-beta. Nature (2000) 13.45

IKK-1 and IKK-2: cytokine-activated IkappaB kinases essential for NF-kappaB activation. Science (1997) 11.89

Wild-type p53 activates transcription in vitro. Nature (1992) 11.39

Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A (2001) 9.40

Genetic inheritance of gene expression in human cell lines. Am J Hum Genet (2004) 8.97

Induction of apoptosis in fibroblasts by IL-1 beta-converting enzyme, a mammalian homolog of the C. elegans cell death gene ced-3. Cell (1993) 7.16

RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease. Nature (1996) 7.04

Smad7 binds to Smurf2 to form an E3 ubiquitin ligase that targets the TGF beta receptor for degradation. Mol Cell (2000) 6.69

Ich-1, an Ice/ced-3-related gene, encodes both positive and negative regulators of programmed cell death. Cell (1994) 5.25

Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat Genet (1998) 4.67

Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol (1991) 4.01

Synapse-specific, long-term facilitation of aplysia sensory to motor synapses: a function for local protein synthesis in memory storage. Cell (1997) 3.93

Murine caspase-11, an ICE-interacting protease, is essential for the activation of ICE. Cell (1998) 3.62

Human cytomegalovirus with IE-2 (UL122) deleted fails to express early lytic genes. J Virol (2001) 3.50

Prevalence of antibodies to human herpesviruses and hepatitis B virus in patients at different stages of human immunodeficiency virus (HIV) infection. Infection (1991) 3.29

Regulation of cardiac gene expression during myocardial growth and hypertrophy: molecular studies of an adaptive physiologic response. FASEB J (1991) 3.29

Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance. J Mol Biol (1982) 3.05

Human magnetic resonance imaging at 8 T. NMR Biomed (1998) 2.96

Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy. J Med Genet (2002) 2.90

Effect of RF coil excitation on field inhomogeneity at ultra high fields: a field optimized TEM resonator. Magn Reson Imaging (2001) 2.84

IL-18-stimulated GADD45 beta required in cytokine-induced, but not TCR-induced, IFN-gamma production. Nat Immunol (2001) 2.81

Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. J Mol Biol (1984) 2.78

A transient, neuron-wide form of CREB-mediated long-term facilitation can be stabilized at specific synapses by local protein synthesis. Cell (1999) 2.77

Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J Mol Biol (1983) 2.75

IkappaB kinase (IKK)-associated protein 1, a common component of the heterogeneous IKK complex. Mol Cell Biol (1999) 2.68

A senescence-like phenotype distinguishes tumor cells that undergo terminal proliferation arrest after exposure to anticancer agents. Cancer Res (1999) 2.67

The Peutz-Jegher gene product LKB1 is a mediator of p53-dependent cell death. Mol Cell (2001) 2.53

MAP kinase translocates into the nucleus of the presynaptic cell and is required for long-term facilitation in Aplysia. Neuron (1997) 2.50

TG101209, a small molecule JAK2-selective kinase inhibitor potently inhibits myeloproliferative disorder-associated JAK2V617F and MPLW515L/K mutations. Leukemia (2007) 2.49

Benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethylketone (Z-VAD.FMK) inhibits apoptosis by blocking the processing of CPP32. Biochem J (1996) 2.46

Receptor-dependent cell stress and amyloid accumulation in systemic amyloidosis. Nat Med (2000) 2.44

An intracellular protein that binds amyloid-beta peptide and mediates neurotoxicity in Alzheimer's disease. Nature (1997) 2.42

Estrogen receptor alpha, not beta, is a critical link in estradiol-mediated protection against brain injury. Proc Natl Acad Sci U S A (2001) 2.40

Role of p53 and p21waf1/cip1 in senescence-like terminal proliferation arrest induced in human tumor cells by chemotherapeutic drugs. Oncogene (1999) 2.34

Transcriptional regulation during cardiac growth and development. Annu Rev Physiol (1993) 2.33

Antibody formation: stimulation by polyadenylic and polycytidylic acids. Science (1967) 2.25

Nitric-oxide dioxygenase activity and function of flavohemoglobins. sensitivity to nitric oxide and carbon monoxide inhibition. J Biol Chem (2000) 2.13

Laryngeal transplantation and 40-month follow-up. N Engl J Med (2001) 2.12

BRUCELLAPHAGE. J Bacteriol (1959) 2.12

Identification of a full-length cDNA for an endogenous retrovirus of miniature swine. J Virol (1998) 2.10

Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations. J Mol Biol (1982) 2.07

Premedication with intravenous dexmedetomidine-midazolam suppresses fentanyl-induced cough. Ir J Med Sci (2012) 2.06

Loss of in vitro metal ion binding specificity in mutant copper-zinc superoxide dismutases associated with familial amyotrophic lateral sclerosis. J Biol Chem (2000) 2.05

Identification and characterization of Ich-3, a member of the interleukin-1beta converting enzyme (ICE)/Ced-3 family and an upstream regulator of ICE. J Biol Chem (1996) 2.05

Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol (1987) 2.04

Geographical and ethnic variation of the 677C>T allele of 5,10 methylenetetrahydrofolate reductase (MTHFR): findings from over 7000 newborns from 16 areas world wide. J Med Genet (2003) 2.03

Validation of lucigenin (bis-N-methylacridinium) as a chemilumigenic probe for detecting superoxide anion radical production by enzymatic and cellular systems. J Biol Chem (1998) 1.99

Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon. Biochim Biophys Acta (1981) 1.95

Beta-COP is essential for transport of protein from the endoplasmic reticulum to the Golgi in vitro. J Cell Biol (1993) 1.88

Interaction between the adhesion receptor, CD44, and the oncogene product, p185HER2, promotes human ovarian tumor cell activation. J Biol Chem (1997) 1.86

Human cytomagalovirus IE1 and IE2 proteins are mutagenic and mediate "hit-and-run" oncogenic transformation in cooperation with the adenovirus E1A proteins. Proc Natl Acad Sci U S A (1997) 1.85

Amyloid-beta peptide-receptor for advanced glycation endproduct interaction elicits neuronal expression of macrophage-colony stimulating factor: a proinflammatory pathway in Alzheimer disease. Proc Natl Acad Sci U S A (1997) 1.82

CD44 interaction with tiam1 promotes Rac1 signaling and hyaluronic acid-mediated breast tumor cell migration. J Biol Chem (2000) 1.79

Pathological changes in human malignant carcinoma treated with high-intensity focused ultrasound. Ultrasound Med Biol (2001) 1.78

Mitochondrial adaptations to obesity-related oxidant stress. Arch Biochem Biophys (2000) 1.74

Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther (2010) 1.74

CD44 interaction with c-Src kinase promotes cortactin-mediated cytoskeleton function and hyaluronic acid-dependent ovarian tumor cell migration. J Biol Chem (2000) 1.72

Secretion of interferon by Bacillus subtilis. Gene (1983) 1.70

Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J Mol Biol (1985) 1.69

A novel role for RIP1 kinase in mediating TNFα production. Cell Death Dis (2012) 1.67

Investigation of the structure of thin HfO(2) films by soft x-ray reflectometry techniques. J Phys Condens Matter (2009) 1.62

A ubiquitous factor (HF-1a) and a distinct muscle factor (HF-1b/MEF-2) form an E-box-independent pathway for cardiac muscle gene expression. Mol Cell Biol (1992) 1.61

Cloning and functional identification of a neuronal glutamine transporter. J Biol Chem (2000) 1.60

Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions. Phys Rev Lett (2011) 1.60

APC2 Cullin protein and APC11 RING protein comprise the minimal ubiquitin ligase module of the anaphase-promoting complex. Mol Biol Cell (2001) 1.59

Comparison of the high-resolution structures of the alpha-amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J Mol Biol (1989) 1.57

Specific cleavage of alpha-fodrin during Fas- and tumor necrosis factor-induced apoptosis is mediated by an interleukin-1beta-converting enzyme/Ced-3 protease distinct from the poly(ADP-ribose) polymerase protease. J Biol Chem (1996) 1.57

Wedelolactone suppresses LPS-induced caspase-11 expression by directly inhibiting the IKK complex. Cell Death Differ (2004) 1.54

ON THE NATURE OF THE SELECTIVE EFFECTS OF DEOXYRIBONUCLEIC ACID DIGESTS UPON PNEUMOCOCCI OF DIFFERENT VIRULENCE. Proc Natl Acad Sci U S A (1958) 1.53

A mathematical model for assessing control strategies against West Nile virus. Bull Math Biol (2005) 1.52

Design and assembly of an 8 tesla whole-body MR scanner. J Comput Assist Tomogr (1999) 1.52

Fluctuation tests with antibody-forming spleen cell populations. Science (1966) 1.51

A novel system A isoform mediating Na+/neutral amino acid cotransport. J Biol Chem (2000) 1.47

Caveolin expression and localization in human keratinocytes suggest a role in lamellar granule biogenesis. J Invest Dermatol (2003) 1.47

FACTORS CONTROLLING BACTERIAL DISSOCIATION. Science (1945) 1.46

Cooperative DNA binding of p53 with TFIID (TBP): a possible mechanism for transcriptional activation. Genes Dev (1993) 1.45

Three-dimensional structure of rabbit liver [Cd7]metallothionein-2a in aqueous solution determined by nuclear magnetic resonance. J Mol Biol (1988) 1.45

Physiologically based pharmacokinetic model for specific and nonspecific monoclonal antibodies and fragments in normal tissues and human tumor xenografts in nude mice. Cancer Res (1994) 1.45

Hyaluronan promotes CD44v3-Vav2 interaction with Grb2-p185(HER2) and induces Rac1 and Ras signaling during ovarian tumor cell migration and growth. J Biol Chem (2001) 1.45

Rho-kinase (ROK) promotes CD44v(3,8-10)-ankyrin interaction and tumor cell migration in metastatic breast cancer cells. Cell Motil Cytoskeleton (1999) 1.45

Quantification of condylar resorption in temporomandibular joint osteoarthritis. Oral Surg Oral Med Oral Pathol Oral Radiol Endod (2010) 1.45

Interferon preparations as modifiers of immune responses. Proc Soc Exp Biol Med (1972) 1.44

[Treatment of acromioclavicular joint separations. Central Kirschner- wire and PDS-augmentation]. Unfallchirurg (1999) 1.43

Bacteria as an Indicator of Formation of Antibodies by Single Spleen Cells in Agar. Science (1965) 1.42

Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at sqrt[S(NN)] =2.76 TeV with the ATLAS detector at the LHC. Phys Rev Lett (2010) 1.41

RNA processing and expression of an intron-encoded protein in yeast mitochondria: role of a conserved dodecamer sequence. Mol Cell Biol (1987) 1.41

Left ventricular myocardial adenosine triphosphate changes during reperfusion of ventricular fibrillation: the influence of flow and epinephrine. Crit Care Med (2000) 1.40

Diagnosis, therapy, and outcome of ventricular septal defects in the 1st year of life: a two-dimensional colour-Doppler echocardiography study. Eur J Pediatr (1990) 1.40

Cytotoxicity of endotoxin in vitro. Effects on macrophages from normal guinea pigs. Aust J Exp Biol Med Sci (1965) 1.39

Measurement of dijet azimuthal decorrelations in pp collisions at sqrt(s)=7  TeV. Phys Rev Lett (2011) 1.39

Hepatocyte growth factor/scatter factor is an autocrine factor for human normal bronchial epithelial and lung carcinoma cells. Cell Growth Differ (1993) 1.36

Adenyl cyclase activity of spleen cells exposed to immunoenhancing synthetic oligo- and polynucleotides. J Immunol (1971) 1.36

Characterization of S-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils. Appl Environ Microbiol (2000) 1.35

Activation of caspase-2 in apoptosis. J Biol Chem (1997) 1.35

Biodistribution of monoclonal antibodies: scale-up from mouse to human using a physiologically based pharmacokinetic model. Cancer Res (1995) 1.35

Determination of the strange-quark density of the proton from ATLAS measurements of the W→ℓν and Z→ℓℓ cross sections. Phys Rev Lett (2012) 1.34

Tumor necrosis factor increases mitochondrial oxidant production and induces expression of uncoupling protein-2 in the regenerating mice [correction of rat] liver. Hepatology (1999) 1.34

Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR (1997) 1.33

In vitro squelching of activated transcription by serum response factor: evidence for a common coactivator used by multiple transcriptional activators. Nucleic Acids Res (1992) 1.33