Published in Protein Sci on June 01, 2001
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
Conformational transition states of a beta-hairpin peptide between the ordered and disordered conformations in explicit water. Protein Sci (2002) 1.58
Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci U S A (2006) 1.22
Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property. Protein Sci (2003) 0.99
Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophys Rev (2012) 0.99
Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters. Protein Sci (2007) 0.91
Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties. Biophys J (2003) 0.90
TAP score: torsion angle propensity normalization applied to local protein structure evaluation. BMC Bioinformatics (2007) 0.87
Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Sci (2011) 0.85
Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent. Biophys J (2005) 0.85
Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects. Biophys J (2008) 0.78
A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. J Mol Model (2013) 0.78
Secondary structure, a missing component of sequence-based minimotif definitions. PLoS One (2012) 0.77
Structural diversity and initial oligomerization of PrP106-126 studied by replica-exchange and conventional molecular dynamics simulations. PLoS One (2014) 0.76
Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding. Biophysics (Nagoya-shi) (2006) 0.75
Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping. Nat Prod Bioprospect (2014) 0.75
Peptide free energy landscapes calibrated by molecular orbital calculations. J Biol Phys (2002) 0.75
Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations. Sci Rep (2016) 0.75
Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins (1995) 14.36
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol (1999) 11.38
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46
Folding dynamics and mechanism of beta-hairpin formation. Nature (1997) 7.30
Emergence of preferred structures in a simple model of protein folding. Science (1996) 4.92
First-principles calculation of the folding free energy of a three-helix bundle protein. Science (1995) 4.19
"New view" of protein folding reconciled with the old through multiple unfolding simulations. Science (1997) 3.93
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc Natl Acad Sci U S A (1999) 3.61
Polymer principles and protein folding. Protein Sci (1999) 3.04
Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins (1998) 3.02
Understanding beta-hairpin formation. Proc Natl Acad Sci U S A (1999) 3.01
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci (1998) 2.94
NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science (1992) 2.83
Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys Rev Lett (1992) 2.41
Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. J Mol Biol (1997) 2.38
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins (1999) 2.25
Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. J Mol Biol (1997) 2.24
Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur J Biochem (1995) 2.15
De novo design and structural analysis of a model beta-hairpin peptide system. Nat Struct Biol (1996) 2.13
Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol (2000) 2.00
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol (1998) 1.85
Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J Mol Biol (2000) 1.74
Structural analysis of non-native states of proteins by NMR methods. Curr Opin Struct Biol (1996) 1.72
Simulations of protein folding and unfolding. Curr Opin Struct Biol (1998) 1.63
A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G. Protein Sci (1999) 1.62
Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet protein. Nat Struct Biol (1996) 1.58
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proc Natl Acad Sci U S A (1997) 1.51
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Sci (1999) 1.51
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb. Nat Struct Biol (1995) 1.46
A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices. J Mol Biol (1996) 1.37
New Monte Carlo algorithm: Entropic sampling. Phys Rev Lett (1993) 1.35
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol (1999) 1.24
The turn sequence directs beta-strand alignment in designed beta-hairpins. Protein Sci (1999) 1.23
Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci (1995) 1.22
Free energy landscapes of peptides by enhanced conformational sampling. J Mol Biol (2000) 1.15
Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics. Protein Sci (1999) 1.08
Lattice simulations of aggregation funnels for protein folding. J Comput Biol (1999) 1.08
Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues. Protein Eng (1996) 1.06
Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide. Proc Natl Acad Sci U S A (1995) 1.04
Protein dynamics determined by backbone conformation and atom packing. Protein Eng (1997) 1.03
Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue. Proteins (1999) 1.00
Monte Carlo simulation and global optimization without parameters. Phys Rev Lett (1995) 0.99
High populations of non-native structures in the denatured state are compatible with the formation of the native folded state. J Mol Biol (1998) 0.97
Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation. J Mol Biol (1998) 0.97
Residual helical and turn structure in the denatured state of staphylococcal nuclease: analysis of peptide fragments. Fold Des (1997) 0.95
Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme. J Mol Biol (1998) 0.94
Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics (1996) 0.94
beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. J Mol Biol (2000) 0.93
The compact and expanded denatured conformations of apomyoglobin in the methanol-water solvent. Protein Sci (1999) 0.93
Molecular dynamics simulations of beta-hairpin folding. Proteins (1999) 0.85
Origin of the designability of protein structures. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics (1999) 0.82
Characterization of flexible molecules in solution: the RGDW peptide. J Mol Biol (1998) 0.78
CHOP is implicated in programmed cell death in response to impaired function of the endoplasmic reticulum. Genes Dev (1998) 11.86
Function of the chemokine receptor CXCR4 in haematopoiesis and in cerebellar development. Nature (1998) 11.41
The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends Microbiol (2001) 7.73
Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature (1994) 6.54
Cloning of mammalian Ire1 reveals diversity in the ER stress responses. EMBO J (1998) 5.96
The Drosophila tuberous sclerosis complex gene homologs restrict cell growth and cell proliferation. Cell (2001) 5.14
Phosphatidylinositol 4-phosphate 5-kinase alpha is a downstream effector of the small G protein ARF6 in membrane ruffle formation. Cell (1999) 4.98
Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci (1994) 4.02
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell (1994) 3.74
Identification of thioredoxin-binding protein-2/vitamin D(3) up-regulated protein 1 as a negative regulator of thioredoxin function and expression. J Biol Chem (1999) 3.67
Ancient linkage groups and frozen accidents. Nature (1973) 3.57
Competitive inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase by ML-236A and ML-236B fungal metabolites, having hypocholesterolemic activity. FEBS Lett (1976) 3.35
Identification of toxin A-negative, toxin B-positive Clostridium difficile by PCR. J Clin Microbiol (1998) 3.34
TLP1: a gene encoding a protein component of mammalian telomerase is a novel member of WD repeats family. Cell (1997) 3.30
Detection of intraoperative incidents by electronic scanning of computerized anesthesia records. Comparison with voluntary reporting. Anesthesiology (1996) 3.28
Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp Cell Res (1986) 3.17
Monoclonal antibodies to Pgp-1/CD44 block lympho-hemopoiesis in long-term bone marrow cultures. J Exp Med (1990) 3.05
Telomerase activation by hTRT in human normal fibroblasts and hepatocellular carcinomas. Nat Genet (1998) 3.01
Identification of novel stress-induced genes downstream of chop. EMBO J (1998) 2.93
Molecular cloning of a porcine gene syk that encodes a 72-kDa protein-tyrosine kinase showing high susceptibility to proteolysis. J Biol Chem (1991) 2.89
Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science (2013) 2.87
Genetic evidence for female host-specific races of the common cuckoo. Nature (2000) 2.84
Collective bulk carrier delocalization driven by electrostatic surface charge accumulation. Nature (2012) 2.80
Familial gastrointestinal stromal tumours with germline mutation of the KIT gene. Nat Genet (1998) 2.80
Putting a new twist on actin: ADF/cofilins modulate actin dynamics. Trends Cell Biol (1999) 2.69
Cupric oxide as an induced-multiferroic with high-TC. Nat Mater (2008) 2.67
Specific localization of serine 19 phosphorylated myosin II during cell locomotion and mitosis of cultured cells. J Cell Biol (1998) 2.64
Isolation and characterization of four plasmids from Bacillus subtilis. J Bacteriol (1977) 2.59
Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J Mol Biol (1995) 2.59
Uterine sutures at prior caesarean section and placenta accreta in subsequent pregnancy: a case-control study. BJOG (2014) 2.56
Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli. Cell (1994) 2.55
Intraoperative hemodynamic predictors of mortality, stroke, and myocardial infarction after coronary artery bypass surgery. Anesth Analg (1999) 2.51
Organization and structure of an E. coli tRNA operon containing seven tRNA genes. Cell (1981) 2.45
Mechanisms involved in valvuloseptal endocardial cushion formation in early cardiogenesis: roles of transforming growth factor (TGF)-beta and bone morphogenetic protein (BMP). Anat Rec (2000) 2.44
ML-236A, ML-236B, and ML-236C, new inhibitors of cholesterogenesis produced by Penicillium citrinium. J Antibiot (Tokyo) (1976) 2.42
Treatment of hemoptysis patients by thrombin and fibrinogen-thrombin infusion therapy using a fiberoptic bronchoscope. Chest (1989) 2.36
Modulation of airway inflammation in cystic fibrosis. In vivo suppression of interleukin-8 levels on the respiratory epithelial surface by aerosolization of recombinant secretory leukoprotease inhibitor. J Clin Invest (1992) 2.33
Matrix metalloproteinases and tissue inhibitors of metalloproteinases in synovial fluids from patients with rheumatoid arthritis or osteoarthritis. Ann Rheum Dis (2000) 2.32
Acriflavine-binding capacity of Escherichia coli in relation to acriflavine sensitivity and metabolic activity. J Bacteriol (1966) 2.28
MID1, a novel Saccharomyces cerevisiae gene encoding a plasma membrane protein, is required for Ca2+ influx and mating. Mol Cell Biol (1994) 2.25
Fc epsilon receptor, a specific differentiation marker transiently expressed on mature B cells before isotype switching. J Exp Med (1986) 2.25
Homophilic complex formation of MT1-MMP facilitates proMMP-2 activation on the cell surface and promotes tumor cell invasion. EMBO J (2001) 2.23
Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci U S A (1992) 2.23
Mutations in the cardiac troponin I gene associated with hypertrophic cardiomyopathy. Nat Genet (1997) 2.20
Interaction of endostatin with integrins implicated in angiogenesis. Proc Natl Acad Sci U S A (2001) 2.19
Heptakis(2,6-O-dimethyl)beta-cyclodextrin: a novel growth stimulant for Bordetella pertussis phase I. J Clin Microbiol (1983) 2.17
Diffusion-weighted imaging of metastatic brain tumors: comparison with histologic type and tumor cellularity. AJNR Am J Neuroradiol (2006) 2.17
Crazy-paving appearance at thin-section CT: spectrum of disease and pathologic findings. Radiology (1999) 2.16
The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem Sci (1995) 2.16
Studies on antioxidants: their carcinogenic and modifying effects on chemical carcinogenesis. Food Chem Toxicol (1987) 2.14
N-acetylcysteine replenishes glutathione in HIV infection. Eur J Clin Invest (2000) 2.13
Genetic determination of resistance to acriflavine, phenethyl alcohol, and sodium dodecyl sulfate in Escherichia coli. J Bacteriol (1968) 2.11
Effect of heptakis (2,6-O-dimethyl) beta-cyclodextrin on the production of pertussis toxin by Bordetella pertussis. Infect Immun (1983) 2.06
Adiponectin suppresses colorectal carcinogenesis under the high-fat diet condition. Gut (2008) 2.05
A gene controlling the synthesis of non specific alkaline phosphatase in Saccharomyces cerevisiae. Biochim Biophys Acta (1976) 2.04
Leukemia cell to endothelial cell communication via exosomal miRNAs. Oncogene (2012) 2.01
Diffusion-weighted single-shot echoplanar MR imaging for liver disease. AJR Am J Roentgenol (1999) 2.00
Solitary fibrous tumour: significance of p53 and CD34 immunoreactivity in its malignant transformation. Histopathology (1998) 2.00
Idiopathic interstitial pneumonias: diagnostic accuracy of thin-section CT in 129 patients. Radiology (1999) 1.99
Distinct roles of thioredoxin in the cytoplasm and in the nucleus. A two-step mechanism of redox regulation of transcription factor NF-kappaB. J Biol Chem (1999) 1.99
Successful nonsurgical management of perforation complicating endoscopic submucosal dissection of gastrointestinal epithelial neoplasms. Endoscopy (2006) 1.97
Actin depolymerizing factor and cofilin phosphorylation dynamics: response to signals that regulate neurite extension. Cell Motil Cytoskeleton (1998) 1.96
Enhanced induction of antitumor T-cell responses by cytotoxic T lymphocyte-associated molecule-4 blockade: the effect is manifested only at the restricted tumor-bearing stages. Cancer Res (1997) 1.94
Local ordering in the pseudogap state of the high-Tc superconductor Bi2Sr2CaCu2O(8+delta). Science (2004) 1.94
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. Proc Natl Acad Sci U S A (2003) 1.92
Insertion of a 5' truncated L1 element into the 3' end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest (1993) 1.92
Novel nonsense mutation in the Na+/HCO3- cotransporter gene (SLC4A4) in a patient with permanent isolated proximal renal tubular acidosis and bilateral glaucoma. J Am Soc Nephrol (2001) 1.90
Fascin, an actin-bundling protein, induces membrane protrusions and increases cell motility of epithelial cells. Mol Biol Cell (1998) 1.86
Nature of the charge distribution in proteins. Nature (1981) 1.85
Thioredoxin, a redox enzyme released in infection and inflammation, is a unique chemoattractant for neutrophils, monocytes, and T cells. J Exp Med (1999) 1.84
A novel pathophysiologic phenomenon in cachexic patients with chronic obstructive pulmonary disease: the relationship between the circadian rhythm of circulating leptin and the very low-frequency component of heart rate variability. Am J Respir Crit Care Med (2001) 1.83
Electronic phase diagram of high-Tc cuprate superconductors from a mapping of the in-plane resistivity curvature. Phys Rev Lett (2004) 1.83
Studies on heterocyclic compounds. 6. Synthesis and analgesic and antiinflammatory activities of 3,4-dimethylpyrano[2,3-c]pyrazol-6-one derivatives. J Med Chem (1984) 1.83
Hereditary amyotrophic lateral sclerosis. Histochemical and electron microscopic study of hyaline inclusions in motor neurons. Arch Neurol (1972) 1.81
A B cell-specific differentiation antigen, CD23, is a receptor for IgE (Fc epsilon R) on lymphocytes. J Immunol (1987) 1.79
Fluorescence energy transfer between Ca2+ transport ATPase molecules in artificial membranes. Biochemistry (1977) 1.78
Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol (1992) 1.78
Prediction of hyperbilirubinemia in near-term and term infants. Pediatrics (2001) 1.77
Correlation between 25-hydroxyvitamin D3 1 alpha-hydroxylase gene expression in alveolar macrophages and the activity of sarcoidosis. Am J Med (2001) 1.77
The relationship between chronic hypoxemia and activation of the tumor necrosis factor-alpha system in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2000) 1.77
The subtypes of localized bronchioloalveolar carcinoma: CT-pathologic correlation in 18 cases. AJR Am J Roentgenol (1999) 1.76
Apolipoprotein E Sendai (arginine 145-->proline): a new variant associated with lipoprotein glomerulopathy. J Am Soc Nephrol (1997) 1.71
The cystic fibrosis gene has a "housekeeping"-type promoter and is expressed at low levels in cells of epithelial origin. J Biol Chem (1991) 1.70
Treatment of hypertensive cerebellar hemorrhage--surgical or conservative management? Neurosurgery (1994) 1.70
Changes in molecular forms of rat hepatic glutathione S-transferase during chemical hepatocarcinogenesis. Cancer Res (1984) 1.69
Expression of eotaxin by human lung epithelial cells: induction by cytokines and inhibition by glucocorticoids. J Clin Invest (1997) 1.69
A novel function of Valpha14+CD4+NKT cells: stimulation of IL-12 production by antigen-presenting cells in the innate immune system. J Immunol (1999) 1.69
Roles of Rho-associated kinase in cytokinesis; mutations in Rho-associated kinase phosphorylation sites impair cytokinetic segregation of glial filaments. J Cell Biol (1998) 1.69
The placental form of glutathione S-transferase as a new marker protein for preneoplasia in rat chemical hepatocarcinogenesis. Gan (1984) 1.68
CHOP-Dependent stress-inducible expression of a novel form of carbonic anhydrase VI. Mol Cell Biol (1999) 1.68
A spore-lytic enzyme released from Bacillus cereus spores during germination. Microbiology (1994) 1.68
Carcinogenicity of butylated hydroxyanisole in F344 rats. J Natl Cancer Inst (1983) 1.68
Angiostatin induces endothelial cell apoptosis and activation of focal adhesion kinase independently of the integrin-binding motif RGD. Proc Natl Acad Sci U S A (1998) 1.66
Tbx5 and the retinotectum projection. Science (2000) 1.65
Exon skipping during splicing of dystrophin mRNA precursor due to an intraexon deletion in the dystrophin gene of Duchenne muscular dystrophy kobe. J Clin Invest (1991) 1.65
Isolation and characterization of Aspergillus parasiticus mutants with impaired aflatoxin production by a novel tip culture method. Appl Environ Microbiol (1988) 1.64
Human 75-kDa DNA-pairing protein is identical to the pro-oncoprotein TLS/FUS and is able to promote D-loop formation. J Biol Chem (1999) 1.64
Fractionation and Purification of Cytochrome C Photooxidase of Spinach. Plant Physiol (1959) 1.64
Specific histocompatibility antigens associated with Behçet's disease. Am J Ophthalmol (1975) 1.63