Published in J Mol Biol on April 08, 2008
Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc (2011) 1.19
Low micromolar zinc accelerates the fibrillization of human tau via bridging of Cys-291 and Cys-322. J Biol Chem (2009) 1.08
Minimal functional sites allow a classification of zinc sites in proteins. PLoS One (2011) 1.02
Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput (2012) 1.01
Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules (2014) 1.00
Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study. J Chem Theory Comput (2009) 0.94
Predicting nonspecific ion binding using DelPhi. Biophys J (2012) 0.91
Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci (2010) 0.85
Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding. Proteins (2013) 0.84
Conformational stability of hepatitis C virus NS3 protease. Biophys J (2010) 0.84
Reactive cysteine in the structural Zn(2+) site of the C1B domain from PKCα. Biochemistry (2012) 0.81
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains. Proc Natl Acad Sci U S A (2009) 0.80
Role of conserved glycine in zinc-dependent medium chain dehydrogenase/reductase superfamily. J Biol Chem (2012) 0.79
Inhibition of a Zn(II)-containing enzyme, alcohol dehydrogenase, by anticancer antibiotics, mithramycin and chromomycin A3. J Biol Inorg Chem (2008) 0.79
NS3 protease from hepatitis C virus: biophysical studies on an intrinsically disordered protein domain. Int J Mol Sci (2013) 0.78
Validation and correction of Zn-CysxHisy complexes. Acta Crystallogr D Struct Biol (2016) 0.78
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. Sci Rep (2015) 0.77
Ion binding to biological macromolecules. Asian J Phys (2014) 0.76
Effect of mutation on the stabilization energy of HIV-1 zinc fingers: a hybrid local self-consistent field/molecular mechanics investigation. J Biol Inorg Chem (2016) 0.75
Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem Rev (2003) 1.95
First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. J Am Chem Soc (2003) 1.45
Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Annu Rev Biophys (2008) 1.43
Zn protein simulations including charge transfer and local polarization effects. J Am Chem Soc (2005) 1.17
Determinants of K+ vs Na+ selectivity in potassium channels. J Am Chem Soc (2009) 1.13
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res (2008) 1.10
Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses. J Phys Chem B (2006) 1.04
Discovering structural motifs using a structural alphabet: application to magnesium-binding sites. BMC Bioinformatics (2007) 1.01
Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins. Acc Chem Res (2007) 1.00
Factors governing the metal coordination number in isolated group IA and IIA metal hydrates. Inorg Chem (2006) 0.99
A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1. J Am Chem Soc (2003) 0.97
Factors governing the Na(+) vs K(+) selectivity in sodium ion channels. J Am Chem Soc (2010) 0.96
Factors governing metal-ligand distances and coordination geometries of metal complexes. J Phys Chem B (2009) 0.95
Competition among metal ions for protein binding sites: determinants of metal ion selectivity in proteins. Chem Rev (2013) 0.95
Competition between Li+ and Mg2+ in metalloproteins. Implications for lithium therapy. J Am Chem Soc (2011) 0.93
Empirical force fields for biologically active divalent metal cations in water. J Phys Chem A (2006) 0.92
A structural-alphabet-based strategy for finding structural motifs across protein families. Nucleic Acids Res (2010) 0.90
Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study. J Am Chem Soc (2005) 0.90
Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins (2007) 0.89
Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study. J Am Chem Soc (2002) 0.89
Competition among Ca2+, Mg2+, and Na+ for model ion channel selectivity filters: determinants of ion selectivity. J Phys Chem B (2012) 0.89
Polarization-consistent versus correlation-consistent basis sets in predicting molecular and spectroscopic properties. J Phys Chem A (2007) 0.88
Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res (2008) 0.87
Why voltage-gated Ca2+ and bacterial Na+ channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity. Phys Chem Chem Phys (2012) 0.85
A DFT/CDM Study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates. J Am Chem Soc (2006) 0.85
Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function. J Phys Chem B (2011) 0.85
Importance of metal hydration on the selectivity of Mg2+ versus Ca2+ in magnesium ion channels. J Am Chem Soc (2013) 0.84
Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study. J Am Chem Soc (2004) 0.84
Mechanism of DNA-binding loss upon single-point mutation in p53. J Biosci (2007) 0.84
Identifying RNA-binding residues based on evolutionary conserved structural and energetic features. Nucleic Acids Res (2013) 0.84
Evolution of eukaryotic ion channels: principles underlying the conversion of Ca²⁺-selective to Na⁺-selective channels. J Am Chem Soc (2014) 0.83
Computational studies of the coordination stereochemistry, bonding, and metal selectivity of mercury. J Phys Chem A (2006) 0.83
Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions. J Comput Chem (2009) 0.83
DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res (2012) 0.83
Redesign of high-affinity nonspecific nucleases with altered sequence preference. J Am Chem Soc (2009) 0.83
Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain. Nucleic Acids Res (2002) 0.83
Ion selectivity strategies of sodium channel selectivity filters. Acc Chem Res (2014) 0.83
Factors controlling the mechanism of NAD(+) non-redox reactions. J Am Chem Soc (2010) 0.82
Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations. J Phys Chem B (2009) 0.82
Factors controlling the reactivity of zinc finger cores. J Am Chem Soc (2011) 0.81
Oxyanion selectivity in sulfate and molybdate transport proteins: an ab initio/CDM study. J Am Chem Soc (2004) 0.81
Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations. J Am Chem Soc (2008) 0.80
An azido-BODIPY probe for glycosylation: initiation of strong fluorescence upon triazole formation. J Am Chem Soc (2014) 0.80
Strategies to model the near-solute solvent molecular density/polarization. J Comput Chem (2009) 0.80
The importance of excluded solvent volume effects in computing hydration free energies. J Phys Chem B (2008) 0.79
Arrangement of 3D structural motifs in ribosomal RNA. Nucleic Acids Res (2010) 0.79
On the charge and molecule based summations of solvent electrostatic potentials and the validity of electrostatic linear response in water. J Biol Phys (2002) 0.79
Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase. J Am Chem Soc (2009) 0.79
GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics. Nucleic Acids Res (2011) 0.78
Toward absolute density of states calculations for proteins. J Phys Chem B (2006) 0.78
Hidden relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding proteins. J Phys Chem B (2012) 0.78
Modeling Zn²⁺ release from metallothionein. J Phys Chem A (2014) 0.78
Reformulation of Maxwell's equations to incorporate near-solute solvent structure. J Phys Chem B (2008) 0.77
Conserved structural motif for recognizing nicotinamide adenine dinucleotide in poly(ADP-ribose) polymerases and ADP-ribosylating toxins: implications for structure-based drug design. J Med Chem (2010) 0.77
Differential role of the protein matrix on the binding of a catalytic aspartate to Mg2+ vs Ca2+: application to ribonuclease H. J Am Chem Soc (2013) 0.76
All-electron calculations of the nucleation structures in metal-induced zinc-finger folding: role of the Peptide backbone. J Am Chem Soc (2007) 0.76
The IgE gene in primates exhibits extraordinary evolutionary diversity. Immunogenetics (2011) 0.76
Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations. J Comput Chem (2014) 0.75
Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study. J Am Chem Soc (2006) 0.75
Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation. J Chem Theory Comput (2016) 0.75
Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition. J Phys Chem B (2006) 0.75
GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics. Nucleic Acids Res (2015) 0.75
Identification of labile Zn sites in drug-target proteins. J Am Chem Soc (2013) 0.75
Comparative effects of human Ig alpha and Ig beta in inducing autoreactive antibodies against B cells in mice. J Immunol (2003) 0.75
Differential effects of the Zn-His-Bkb vs Zn-His-[Asp/Glu] triad on Zn-core stability and reactivity. J Am Chem Soc (2005) 0.75
Factors governing intrinsic chemical reactivity differences between clavulanic and penicillanic acids. J Am Chem Soc (2002) 0.75
Protein/solvent medium effects on Mg(2+)-carboxylate interactions in metalloenzymes. J Am Chem Soc (2010) 0.75