Published in Chem Asian J on February 03, 2011
Glycyrrhizin binds to high-mobility group box 1 protein and inhibits its cytokine activities. Chem Biol (2007) 3.12
A novel role for HMGB1 in TLR9-mediated inflammatory responses to CpG-DNA. Blood (2007) 3.09
Swe1Wee1-dependent tyrosine phosphorylation of Hsp90 regulates distinct facets of chaperone function. Mol Cell (2010) 2.24
The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep (2008) 2.22
Rational design of shepherdin, a novel anticancer agent. Cancer Cell (2005) 1.74
Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90. J Clin Invest (2009) 1.72
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc Natl Acad Sci U S A (2002) 1.64
Defective glucose metabolism in polycystic kidney disease identifies a new therapeutic strategy. Nat Med (2013) 1.62
NMR structure of the first PHD finger of autoimmune regulator protein (AIRE1). Insights into autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) disease. J Biol Chem (2005) 1.47
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation. Nucleic Acids Res (2009) 1.46
Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology. Chem Biol (2013) 1.45
Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer. PLoS Comput Biol (2009) 1.43
The long acidic tail of high mobility group box 1 (HMGB1) protein forms an extended and flexible structure that interacts with specific residues within and between the HMG boxes. Biochemistry (2004) 1.24
The stem cell secretome and its role in brain repair. Biochimie (2013) 1.19
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18
Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins (2004) 1.09
Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 1.07
Antileukemic activity of shepherdin and molecular diversity of hsp90 inhibitors. J Natl Cancer Inst (2006) 1.06
Structural properties of Gerstmann-Straussler-Scheinker disease amyloid protein. J Biol Chem (2003) 1.06
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol (2005) 1.04
Structural basis for the interaction of isoDGR with the RGD-binding site of alphavbeta3 integrin. J Biol Chem (2008) 1.03
Small-molecule targeting of heat shock protein 90 chaperone function: rational identification of a new anticancer lead. J Med Chem (2006) 1.03
Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations. PLoS Comput Biol (2012) 1.01
Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion. PLoS One (2009) 1.01
Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci (2004) 1.00
Dynamic diagnosis of familial prion diseases supports the β2-α2 loop as a universal interference target. PLoS One (2011) 0.98
Understanding ligand-based modulation of the Hsp90 molecular chaperone dynamics at atomic resolution. Proc Natl Acad Sci U S A (2008) 0.98
Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study. Protein Sci (2005) 0.97
Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations. PLoS Comput Biol (2012) 0.97
Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin. FEBS Lett (2003) 0.96
Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. Proteins (2008) 0.96
Targeting tumor angiogenesis with TSP-1-based compounds: rational design of antiangiogenic mimetics of endogenous inhibitors. Oncotarget (2010) 0.96
Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study. PLoS One (2012) 0.96
AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome. Nucleic Acids Res (2012) 0.95
Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations. Biophys J (2008) 0.95
The structural intolerance of the PrP alpha-fold for polar substitution of the helix-3 methionines. Cell Mol Life Sci (2010) 0.95
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J (2010) 0.95
Exploiting antigenic diversity for vaccine design: the chlamydia ArtJ paradigm. J Biol Chem (2010) 0.94
Misfolding of the amyloid beta-protein: a molecular dynamics study. Proteins (2006) 0.94
Metabolomics of B to plasma cell differentiation. J Proteome Res (2011) 0.93
Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem (2010) 0.91
Redox potential of quinones in photosynthetic reaction centers from Rhodobacter sphaeroides: dependence on protonation of Glu-L212 and Asp-L213. Biochemistry (2003) 0.90
Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif. Mol Immunol (2005) 0.90
Structural determinants of the unusual helix stability of a de novo engineered vascular endothelial growth factor (VEGF) mimicking peptide. Chemistry (2008) 0.89
Pharmacological enhancement of α-glucosidase by the allosteric chaperone N-acetylcysteine. Mol Ther (2012) 0.89
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35. PLoS Comput Biol (2011) 0.89
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics (2005) 0.88
Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein. Proteins (2005) 0.87
Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation. Biochemistry (2002) 0.87
Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides. Chemistry (2003) 0.87
Molecular dynamics simulations of proteins and peptides: from folding to drug design. Curr Protein Pept Sci (2008) 0.86
3D-QSAR Assisted Design, Synthesis and Evaluation of Novobiocin Analogues. ACS Med Chem Lett (2012) 0.86
Modeling the alpha-helix to beta-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Abeta(12-28): insights from all-atom molecular dynamics simulations. J Mol Graph Model (2004) 0.86
Nephrocystin-1 forms a complex with polycystin-1 via a polyproline motif/SH3 domain interaction and regulates the apoptotic response in mammals. PLoS One (2010) 0.86
Rational epitope design for protein targeting. ACS Chem Biol (2012) 0.85
Safety and efficacy of transcranial direct current stimulation in acute experimental ischemic stroke. Stroke (2013) 0.84
A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen. Structure (2012) 0.84
Interactions of the C2 domain of human factor V with a model membrane. Proteins (2006) 0.83
Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations. J Phys Chem B (2005) 0.83
Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry (2010) 0.83
Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule. PLoS One (2012) 0.82
Updated management of non-st-segment elevation acute coronary syndromes: selection of patients for low-cost care: an analysis of outcome and cost effectiveness. Med Sci Monit (2005) 0.81
Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations. J Chem Inf Model (2013) 0.81
Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities. J Chem Inf Model (2014) 0.81
Identification of domains in protein structures from the analysis of intramolecular interactions. J Phys Chem B (2012) 0.81
Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics. Biophys Chem (2009) 0.81
Fast three dimensional pharmacophore virtual screening of new potent non-steroid aromatase inhibitors. J Med Chem (2009) 0.81
Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1. FEBS J (2013) 0.81
Protein and lipid interactions driving molecular mechanisms of in meso crystallization. J Am Chem Soc (2014) 0.81
Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study. J Biol Inorg Chem (2005) 0.81
Deforestation and the structure of frog communities in the Humedale Terraba-Sierpe, Costa Rica. Zoolog Sci (2009) 0.81
Why is a protective antigen protective? Hum Vaccin (2009) 0.80
Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens. J Virol (2008) 0.80
Cost utility and budget impact of third-generation aromatase inhibitors for advanced breast cancer: a literature-based model analysis of costs in the Italian National Health Service. Clin Ther (2004) 0.80
Structural and computational biology of the molecular chaperone Hsp90: from understanding molecular mechanisms to computer-based inhibitor design. Curr Top Med Chem (2009) 0.80
A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation. J Mol Biol (2008) 0.80
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes. BMC Struct Biol (2010) 0.80
Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations. Biochemistry (2014) 0.80
Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols. ChemMedChem (2007) 0.80
An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors. Eur J Med Chem (2009) 0.79
Oxidation-induced structural changes of ceruloplasmin foster NGR motif deamidation that promotes integrin binding and signaling. J Biol Chem (2013) 0.79
Investigating allostery in molecular recognition: insights from a computational study of multiple antibody-antigen complexes. J Phys Chem B (2013) 0.79
Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins. BMC Struct Biol (2006) 0.79
Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition. Methods Mol Biol (2009) 0.78
2D TR-NOESY experiments interrogate and rank ligand-receptor interactions in living human cancer cells. Angew Chem Int Ed Engl (2010) 0.78
Structure determination and dynamics of peptides overlapping the catalytic hairpin of the Ras-specific GEF Cdc25(Mm). Biochemistry (2003) 0.78
Structural analysis of a helical peptide unfolding pathway. Chemistry (2010) 0.78
Identification of TMPRSS6 cleavage sites of hemojuvelin. J Cell Mol Med (2015) 0.78
From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. FEBS J (2015) 0.78