Published in Biophys J on April 25, 2008
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophys J (2009) 1.61
Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins (2012) 0.83
Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA. J Phys Chem B (2010) 0.81
TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance. Biophys J (2010) 0.80
Synergistic applications of MD and NMR for the study of biological systems. J Biomed Biotechnol (2012) 0.79
Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations. Eur Biophys J (2015) 0.75
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J (2005) 2.84
Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme. Biochemistry (1995) 2.31
Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res (2002) 2.24
Flexibility and packing in proteins. Proc Natl Acad Sci U S A (2002) 2.22
General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation. J Am Chem Soc (2002) 2.18
A refined solution structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci (2001) 1.88
Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme. J Biomol NMR (2004) 1.76
Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data. Proteins (2000) 1.53
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr Opin Struct Biol (2003) 1.50
Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes. Biochemistry (1995) 1.17
Characterizing global substates of myoglobin. Structure (1998) 1.08
Dynamics of the Hck-SH3 domain: comparison of experiment with multiple molecular dynamics simulations. Protein Sci (2000) 0.92
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Long-range interactions within a nonnative protein. Science (2002) 4.06
NMR spectroscopy of RNA. Chembiochem (2003) 2.49
Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 2.41
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc Natl Acad Sci U S A (2005) 2.07
Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. J Am Chem Soc (2007) 2.03
Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov (2008) 1.95
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res (2006) 1.78
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem (2005) 1.68
NMR characterization of kinase p38 dynamics in free and ligand-bound forms. Angew Chem Int Ed Engl (2006) 1.61
A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nat Methods (2012) 1.56
Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain. Nucleic Acids Res (2007) 1.44
Time-resolved NMR studies of RNA folding. Biopolymers (2007) 1.40
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc Natl Acad Sci U S A (2007) 1.39
Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding. Curr Med Chem (2006) 1.37
Molecular mechanism of inhibition of the human protein complex Hsp90-Cdc37, a kinome chaperone-cochaperone, by triterpene celastrol. Angew Chem Int Ed Engl (2009) 1.34
Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution. Nucleic Acids Res (2010) 1.30
Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings. J Am Chem Soc (2003) 1.25
Blind testing of routine, fully automated determination of protein structures from NMR data. Structure (2012) 1.23
Three-state mechanism couples ligand and temperature sensing in riboswitches. Nature (2013) 1.21
Translation on demand by a simple RNA-based thermosensor. Nucleic Acids Res (2010) 1.20
Solution NMR structure of proteorhodopsin. Angew Chem Int Ed Engl (2011) 1.15
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res (2009) 1.14
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J Mol Biol (2003) 1.13
Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol (2009) 1.13
Kinetics of photoinduced RNA refolding by real-time NMR spectroscopy. Angew Chem Int Ed Engl (2005) 1.12
DrugScoreRNA--knowledge-based scoring function to predict RNA-ligand interactions. J Chem Inf Model (2007) 1.11
Structure of Aquifex aeolicus argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function. J Biol Chem (2006) 1.10
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Nucleic Acids Res (2006) 1.10
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res (2010) 1.10
NMR backbone assignment of a protein kinase catalytic domain by a combination of several approaches: application to the catalytic subunit of cAMP-dependent protein kinase. Chembiochem (2004) 1.10
Molecular recognition of RNA: challenges for modelling interactions and plasticity. J Mol Recognit (2010) 1.10
Discovery of a new class of inhibitors of Mycobacterium tuberculosis protein tyrosine phosphatase B by biology-oriented synthesis. Angew Chem Int Ed Engl (2008) 1.09
Protein rigidity and thermophilic adaptation. Proteins (2011) 1.09
Brunsvicamides A-C: sponge-related cyanobacterial peptides with Mycobacterium tuberculosis protein tyrosine phosphatase inhibitory activity. J Med Chem (2006) 1.09
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res (2012) 1.08
NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops. Nucleic Acids Res (2008) 1.07
Analyzing the flexibility of RNA structures by constraint counting. Biophys J (2008) 1.07
Mapping the landscape of RNA dynamics with NMR spectroscopy. Acc Chem Res (2011) 1.06
Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants. J Am Chem Soc (2010) 1.06
The molecular mechanism of spider-silk formation. Angew Chem Int Ed Engl (2010) 1.06
Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy. J Biomol NMR (2007) 1.06
Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res (2010) 1.05
Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study. Structure (2005) 1.04
The structure of the cytochrome p450cam-putidaredoxin complex determined by paramagnetic NMR spectroscopy and crystallography. J Mol Biol (2013) 1.04
Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR 13C relaxation. J Biomol NMR (2005) 1.04
Glutamic acid-rich proteins of rod photoreceptors are natively unfolded. J Biol Chem (2005) 1.04
Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins (2006) 1.03
Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR. Proc Natl Acad Sci U S A (2004) 1.03
Retroviral vectors pseudotyped with severe acute respiratory syndrome coronavirus S protein. J Virol (2004) 1.03
Engineering encodable lanthanide-binding tags into loop regions of proteins. J Am Chem Soc (2011) 1.02
Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties. Cancer Cell (2013) 1.01
Enantioselective total synthesis of cylindramide. Angew Chem Int Ed Engl (2005) 1.01
NMR analysis of a Tau phosphorylation pattern. J Am Chem Soc (2006) 1.00
The human Cdc37.Hsp90 complex studied by heteronuclear NMR spectroscopy. J Biol Chem (2008) 1.00
Tandem phosphorylation of serines 221 and 318 by protein kinase Cdelta coordinates mRNA binding and nucleocytoplasmic shuttling of HuR. Mol Cell Biol (2010) 0.99
Angular dependence of 1J(Ni,Calphai) and 2J(Ni,Calpha(i-1)) coupling constants measured in J-modulated HSQCs. J Biomol NMR (2002) 0.99
Double-lanthanide-binding tags: design, photophysical properties, and NMR applications. J Am Chem Soc (2007) 0.97
Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J Chem Inf Model (2011) 0.97
Modulation of the stability of the Salmonella fourU-type RNA thermometer. Nucleic Acids Res (2011) 0.97
Discovery of Mycobacterium tuberculosis protein tyrosine phosphatase A (MptpA) inhibitors based on natural products and a fragment-based approach. Chembiochem (2005) 0.96
Double-lanthanide-binding tags for macromolecular crystallographic structure determination. J Am Chem Soc (2007) 0.95
Histone deacetylase (HDAC) inhibitors with a novel connecting unit linker region reveal a selectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells. J Med Chem (2013) 0.95
A caged uridine for the selective preparation of an RNA fold and determination of its refolding kinetics by real-time NMR. Chembiochem (2006) 0.95
A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model (2011) 0.95
Total synthesis and NMR investigations of cylindramide. Chemistry (2006) 0.95
Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res (2013) 0.95
Motional properties of unfolded ubiquitin: a model for a random coil protein. J Biomol NMR (2006) 0.95
New NMR experiments for RNA nucleobase resonance assignment and chemical shift analysis of an RNA UUCG tetraloop. J Biomol NMR (2004) 0.94
Constraint counting on RNA structures: linking flexibility and function. Methods (2009) 0.93
NMR backbone assignment of the mitogen-activated protein (MAP) kinase p38. J Biomol NMR (2005) 0.93
Identification of inhibitors for mycobacterial protein tyrosine phosphatase B (MptpB) by biology-oriented synthesis (BIOS). Chem Asian J (2007) 0.92
Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch. Chembiochem (2006) 0.91
Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex. EMBO J (2006) 0.91
Optimization of transversal relaxation of nitroxides for pulsed electron-electron double resonance spectroscopy in phospholipid membranes. J Phys Chem B (2010) 0.91
Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell (2013) 0.91
Experimental evidence for proton motive force-dependent catalysis by the diheme-containing succinate:menaquinone oxidoreductase from the Gram-positive bacterium Bacillus licheniformis. Biochemistry (2006) 0.91
Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function. J Chem Inf Model (2013) 0.90
Mutations in gp120 contribute to the resistance of human immunodeficiency virus type 1 to membrane-anchored C-peptide maC46. J Virol (2009) 0.90
The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. J Struct Biol (2012) 0.90
Structure-based computational analysis of protein binding sites for function and druggability prediction. J Biotechnol (2011) 0.89
Modulation of compactness and long-range interactions of unfolded lysozyme by single point mutations. Angew Chem Int Ed Engl (2004) 0.89
Combined solid state and solution NMR studies of alpha,epsilon-15N labeled bovine rhodopsin. J Biomol NMR (2007) 0.89
Model development for the viral Kcv potassium channel. Biophys J (2009) 0.89
Structure induction of the T-cell receptor zeta-chain upon lipid binding investigated by NMR spectroscopy. Chembiochem (2007) 0.89
Characterization of the unfolded state of bovine alpha-lactalbumin and comparison with unfolded states of homologous proteins. Protein Sci (2006) 0.89
Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity. Blood (2010) 0.89
Structure and dynamics of the deoxyguanosine-sensing riboswitch studied by NMR-spectroscopy. Nucleic Acids Res (2011) 0.89
NMR spectroscopic detection of protein protons and longitudinal relaxation rates between 0.01 and 50 MHz. Angew Chem Int Ed Engl (2005) 0.88
FEW: a workflow tool for free energy calculations of ligand binding. J Comput Chem (2013) 0.88
Individual basepair stability of DNA and RNA studied by NMR-detected solvent exchange. Biophys J (2012) 0.88
The state of the art of chemical biology. Chembiochem (2009) 0.88
CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res (2013) 0.88
Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy. J Am Chem Soc (2007) 0.88
Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy. J Am Chem Soc (2009) 0.88
Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins (2010) 0.87
Small-molecule binding sites on proteins established by paramagnetic NMR spectroscopy. J Am Chem Soc (2013) 0.87
Photo-CIDNP reveals differences in compaction of non-native states of lysozyme. J Am Chem Soc (2006) 0.87
Unfolded-state structure and dynamics influence the fibril formation of human prion protein. Angew Chem Int Ed Engl (2009) 0.86