Published in J Chem Theory Comput on January 02, 2012
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. J Chem Theory Comput (2013) 1.65
Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput (2013) 1.22
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model (2014) 0.87
Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B (2014) 0.83
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field. J Chem Theory Comput (2014) 0.82
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J Comput Chem (2016) 0.81
Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr (2014) 0.80
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B (2014) 0.78
Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis. Front Mol Biosci (2015) 0.77
Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism. BMC Struct Biol (2014) 0.77
Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem (2014) 0.76
Fragment-Based Identification of Influenza Endonuclease Inhibitors. J Med Chem (2016) 0.75
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des (2017) 0.75
Metal Ion Modeling Using Classical Mechanics. Chem Rev (2017) 0.75
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
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J Comput Chem (2017) 0.75
Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations. J Phys Chem B (2017) 0.75
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature (2005) 19.15
The biochemical basis of zinc physiology. Physiol Rev (1993) 6.59
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure (1996) 5.30
Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct (1999) 4.81
Recent Advances in Zinc Enzymology. Chem Rev (1996) 4.28
Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc (2003) 3.56
Matrix metalloproteinase inhibitors as therapy for inflammatory and vascular diseases. Nat Rev Drug Discov (2007) 3.36
Structural basis for AMP binding to mammalian AMP-activated protein kinase. Nature (2007) 3.26
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem (2002) 3.11
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
Synthetic analogues relevant to the structure and function of zinc enzymes. Chem Rev (2004) 2.64
Tuning ion coordination architectures to enable selective partitioning. Biophys J (2007) 2.38
Structural basis for the highly selective inhibition of MMP-13. Chem Biol (2005) 2.33
Binuclear Metallohydrolases. Chem Rev (1996) 2.07
Structural biology of zinc. Adv Protein Chem (1991) 1.92
Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A (2008) 1.75
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B (2006) 1.73
Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins (1995) 1.72
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys (2006) 1.69
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput (2011) 1.55
Intracellular zinc homeostasis and zinc signaling. Cancer Sci (2008) 1.52
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem (2009) 1.46
Structure and dynamics of calmodulin in solution. Biophys J (1998) 1.27
Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs. Biochimie (2005) 1.26
Zn protein simulations including charge transfer and local polarization effects. J Am Chem Soc (2005) 1.17
A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc (2004) 1.15
Metal-binding sites in proteins. Curr Opin Biotechnol (1991) 1.15
Matrix metalloproteinase inhibitors as prospective agents for the prevention and treatment of cardiovascular and neoplastic diseases. Curr Top Med Chem (2006) 1.12
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem (2005) 1.10
Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures. Biochim Biophys Acta (2007) 1.10
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. J Comput Chem (2003) 1.09
Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. J Chem Theory Comput (2010) 1.07
Matrix metalloproteinases as drug targets in ischemia/reperfusion injury. Drug Discov Today (2011) 1.04
Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. J Am Chem Soc (2007) 1.03
Physical basis of structural and catalytic Zn-binding sites in proteins. J Mol Biol (2008) 1.01
Extra binding region induced by non-zinc chelating inhibitors into the S1' subsite of matrix metalloproteinase 8 (MMP-8). J Med Chem (2009) 1.01
Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals. J Chem Theory Comput (2011) 1.00
Structure-based design and synthesis of novel non-zinc chelating MMP-12 inhibitors. Bioorg Med Chem Lett (2005) 1.00
Multipole electrostatics in hydration free energy calculations. J Comput Chem (2010) 1.00
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. J Comput Chem (2005) 0.97
Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallogr D Biol Crystallogr (2009) 0.97
Quasichemical and structural analysis of polarizable anion hydration. J Chem Phys (2010) 0.95
Metal-coupled folding of Cys2His2 zinc-finger. J Am Chem Soc (2007) 0.95
Molecular simulations of ion channels: a quantum chemist's perspective. J Gen Physiol (2010) 0.94
Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit (2010) 0.93
Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein Sci (2010) 0.92
Polarization and charge transfer in the hydration of chloride ions. J Chem Phys (2010) 0.92
Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site. Phys Chem Chem Phys (2008) 0.91
Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. Biophys J (2010) 0.91
Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. Biophys J (2010) 0.89
Making a new turn in matrix metalloprotease inhibition. Chem Biol (2005) 0.88
Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases. J Phys Chem B (2006) 0.87
Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem (2002) 0.86
Binding affinity of hydroxamate inhibitors of matrix metalloproteinase-2. J Mol Model (2004) 0.86
Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase. J Am Chem Soc (2010) 0.86
Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chem Biol Drug Des (2011) 0.86
Calculation and prediction of binding free energies for the matrix metalloproteinases. J Med Chem (2000) 0.85
Synthesis of a series of stromelysin-selective thiadiazole urea matrix metalloproteinase inhibitors. J Med Chem (1999) 0.85
Molecular dynamics simulations of peptide carboxylate hydration. Phys Chem Chem Phys (2006) 0.85
Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase. J Med Chem (1999) 0.85
Molecular dynamics study of the hydration of lanthanum(III) and europium(III) including many-body effects. J Phys Chem B (2005) 0.84
Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates. J Phys Chem B (2011) 0.82
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem (2007) 0.82
Force Field Modeling of Amino Acid Conformational Energies. J Chem Theory Comput (2007) 0.82
Interaction of viral proteins with metal ions: role in maintaining the structure and functions of viruses. FEMS Immunol Med Microbiol (2005) 0.81
Design of zinc binding functions for carbonic anhydrase inhibitors. Curr Pharm Des (2008) 0.80
Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field. J Mol Graph Model (2005) 0.80
Gd(III) polyaminocarboxylate chelate: realistic many-body molecular dynamics simulations for molecular imaging applications. J Phys Chem B (2006) 0.79
The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins (2011) 0.79
Modeling of inhibitor-metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry. Proteins (1998) 0.78
The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study. Phys Chem Chem Phys (2010) 0.76
Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study. J Phys Chem B (2007) 0.76
H2S as a physiologic vasorelaxant: hypertension in mice with deletion of cystathionine gamma-lyase. Science (2008) 7.89
Fibroblast growth factor 23 and risks of mortality and end-stage renal disease in patients with chronic kidney disease. JAMA (2011) 5.86
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell (2005) 5.43
A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA (2011) 4.63
RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature (2007) 4.35
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature (2005) 3.67
UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell (2006) 3.65
Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc (2003) 3.56
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα. Cell (2013) 2.87
Tight junction proteins claudin-1 and occludin control hepatitis C virus entry and are downregulated during infection to prevent superinfection. J Virol (2008) 2.84
Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol Cell (2007) 2.71
Structure and mechanism of human DNA polymerase eta. Nature (2010) 2.69
Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J Biol Chem (2010) 2.59
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems. Proc Natl Acad Sci U S A (2008) 2.56
The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci U S A (2007) 2.53
Periconceptional dietary intake of choline and betaine and neural tube defects in offspring. Am J Epidemiol (2004) 2.49
Urine neutrophil gelatinase-associated lipocalin levels do not improve risk prediction of progressive chronic kidney disease. Kidney Int (2013) 2.48
Inflammatory breast cancer: the disease, the biology, the treatment. CA Cancer J Clin (2010) 2.45
Estimating GFR among participants in the Chronic Renal Insufficiency Cohort (CRIC) Study. Am J Kidney Dis (2012) 2.42
Use of abdominopelvic computed tomography in emergency departments and rates of urgent diagnoses in Crohn's disease. Clin Gastroenterol Hepatol (2011) 2.40
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J (2005) 2.37
Small molecule integrin antagonists that bind to the beta2 subunit I-like domain and activate signals in one direction and block them in the other. Immunity (2003) 2.34
Gamma-secretase gene mutations in familial acne inversa. Science (2010) 2.30
Relationship of estimated GFR and coronary artery calcification in the CRIC (Chronic Renal Insufficiency Cohort) Study. Am J Kidney Dis (2011) 2.25
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J (2006) 2.23
The primacy of affinity over clustering in regulation of adhesiveness of the integrin {alpha}L{beta}2. J Cell Biol (2004) 2.22
NCIPLOT: a program for plotting non-covalent interaction regions. J Chem Theory Comput (2011) 2.17
Delays in primary surgical treatment are not associated with significant tumor size progression in breast cancer patients. Ann Surg (2011) 2.16
Gene transfer to plants by diverse species of bacteria. Nature (2005) 2.11
Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol Cell (2004) 2.10
Association of serum bicarbonate with risk of renal and cardiovascular outcomes in CKD: a report from the Chronic Renal Insufficiency Cohort (CRIC) study. Am J Kidney Dis (2013) 2.09
Replication of a cis-syn thymine dimer at atomic resolution. Nature (2003) 2.07
Oncosome formation in prostate cancer: association with a region of frequent chromosomal deletion in metastatic disease. Cancer Res (2009) 2.07
Chimpanzee adenovirus antibodies in humans, sub-Saharan Africa. Emerg Infect Dis (2006) 1.99
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci U S A (2010) 1.96
Black soot and the survival of Tibetan glaciers. Proc Natl Acad Sci U S A (2009) 1.93
Multidisciplinary considerations in the implementation of the findings from the American College of Surgeons Oncology Group (ACOSOG) Z0011 study: a practice-changing trial. Ann Surg Oncol (2011) 1.93
Watching DNA polymerase η make a phosphodiester bond. Nature (2012) 1.92
Liposomal doxorubicin increases radiofrequency ablation-induced tumor destruction by increasing cellular oxidative and nitrative stress and accelerating apoptotic pathways. Radiology (2010) 1.84
Fibroblast growth factor-23 and cardiovascular events in CKD. J Am Soc Nephrol (2013) 1.78
Brain tissue oxygen and outcome after severe traumatic brain injury: a systematic review. Crit Care Med (2009) 1.75
Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A (2008) 1.75
Metabolic syndrome meets osteoarthritis. Nat Rev Rheumatol (2012) 1.75
118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. BMC Med Genet (2009) 1.74
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B (2006) 1.73
Reduced risks of neural tube defects and orofacial clefts with higher diet quality. Arch Pediatr Adolesc Med (2011) 1.73
A multilevel adaptive finite element algorithm for bioluminescence tomography. Opt Express (2006) 1.71
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys (2006) 1.69
Association of cardiac troponin T with left ventricular structure and function in CKD. Am J Kidney Dis (2013) 1.67
Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. Proc Natl Acad Sci U S A (2004) 1.66
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. J Chem Theory Comput (2013) 1.65
Large liver tumors: protocol for radiofrequency ablation and its clinical application in 110 patients--mathematic model, overlapping mode, and electrode placement process. Radiology (2004) 1.65
Adherence to a healthy lifestyle and all-cause mortality in CKD. Clin J Am Soc Nephrol (2013) 1.64
Predicting the extent of nodal disease in early-stage breast cancer. Ann Surg Oncol (2014) 1.63
Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. EMBO J (2004) 1.61
High-affinity peptide against MT1-MMP for in vivo tumor imaging. J Control Release (2011) 1.59
Crystal structure of T4 endonuclease VII resolving a Holliday junction. Nature (2007) 1.59
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput (2007) 1.58
H2S, endoplasmic reticulum stress, and apoptosis of insulin-secreting beta cells. J Biol Chem (2007) 1.56
Orofacial clefts in the National Birth Defects Prevention Study, 1997-2004. Am J Med Genet A (2009) 1.55
In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombination. DNA Repair (Amst) (2003) 1.55
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell (2005) 1.55
Treatment of pregnant breast cancer patients and outcomes of children exposed to chemotherapy in utero. Cancer (2006) 1.54
Mid-pregnancy cotinine and risks of orofacial clefts and neural tube defects. J Pediatr (2008) 1.52
An enzymatic atavist revealed in dual pathways for water activation. PLoS Biol (2008) 1.52
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol (2013) 1.52
Bcl11a is essential for lymphoid development and negatively regulates p53. J Exp Med (2012) 1.51
History-adjusted marginal structural analysis of the association between hemoglobin variability and mortality among chronic hemodialysis patients. Clin J Am Soc Nephrol (2008) 1.49
Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication. J Biol Chem (2004) 1.48
Reconstruction of chemically burned rat corneal surface by bone marrow-derived human mesenchymal stem cells. Stem Cells (2005) 1.46
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem (2009) 1.46
A more precise HIV integration assay designed to detect small differences finds lower levels of integrated DNA in HAART treated patients. Virology (2008) 1.45
Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin. Proc Natl Acad Sci U S A (2012) 1.44
Intermolecular electrostatic energies using density fitting. J Chem Phys (2005) 1.42
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc (2011) 1.42
Development of new cancers in patients with DCIS: the M.D. Anderson experience. Ann Surg Oncol (2007) 1.42
Brain hyperthermia after traumatic brain injury does not reduce brain oxygen. Neurosurgery (2008) 1.42
Inflammatory breast cancer: what we know and what we need to learn. Oncologist (2012) 1.41
Air pollution and birth weight in northern Nevada, 1991-1999. Inhal Toxicol (2002) 1.41
Systematic identification of microRNA and messenger RNA profiles in hepatitis C virus-infected human hepatoma cells. Virology (2009) 1.40
Structural insight into translesion synthesis by DNA Pol II. Cell (2009) 1.39
Mutations in PRRT2 result in paroxysmal dyskinesias with marked variability in clinical expression. J Med Genet (2011) 1.38
Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota. J Biol Chem (2004) 1.37
PRC2 complexes with JARID2, MTF2, and esPRC2p48 in ES cells to modulate ES cell pluripotency and somatic cell reprogramming. Stem Cells (2011) 1.37
Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface. J Chem Phys (2007) 1.35
Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. J Chem Phys (2006) 1.34
Product-assisted catalysis in base-excision DNA repair. Nat Struct Biol (2003) 1.34
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J Chem Phys (2007) 1.33
SUMO2/3 conjugation is an endogenous neuroprotective mechanism. J Cereb Blood Flow Metab (2011) 1.32
A phase I study of oral panobinostat alone and in combination with docetaxel in patients with castration-resistant prostate cancer. Cancer Chemother Pharmacol (2010) 1.32
Systematic improvement of a classical molecular model of water. J Phys Chem B (2013) 1.31
Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling. J Chem Phys (2009) 1.31
Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops. Nat Struct Mol Biol (2011) 1.31
Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production. J Am Chem Soc (2012) 1.30
Identification of prognosis-relevant subgroups in patients with chemoresistant triple-negative breast cancer. Clin Cancer Res (2013) 1.30
Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins. Proteins (2006) 1.29
Treatment efficacy of radiofrequency ablation of 338 patients with hepatic malignant tumor and the relevant complications. World J Gastroenterol (2005) 1.28
Rational design of protein-based MRI contrast agents. J Am Chem Soc (2008) 1.28