Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos

scientific article published on 18 March 2015

Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.3390/IJMS16036217
P8608Fatcat IDrelease_7jh7dmsmknd2da6znfotnxcwtu
P932PMC publication ID4394528
P698PubMed publication ID25794283
P5875ResearchGate publication ID276933303

P2093author name stringDongmei Wang
Zhenhuan Zhou
Hanyong Jin
Weiwei Han
Shanshan Guan
P2860cites workFree energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulationsQ87365245
The conserved N-terminal helix of acylpeptide hydrolase from archaeon Aeropyrum pernix K1 is important for its hyperthermophilic activityQ47603215
Multiwfn: a multifunctional wavefunction analyzer.Q48564792
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.Q48785859
Molecular Dynamics of Organophosphorous Hydrolases Bound to the Nerve Agent Soman.Q50966404
Regularized linearization for quantum nonlinear optical cavities: application to degenerate optical parametric oscillators.Q51023776
Discrimination of esterase and peptidase activities of acylaminoacyl peptidase from hyperthermophilic Aeropyrum pernix K1 by a single mutation.Q51212407
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.Q51638510
Optimized Potential of Mean Force Calculations for Standard Binding Free Energies.Q53420974
Understanding the molecular basis of MK2-p38α signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies.Q54507909
A novel class of protease targets of phosphatidylethanolamine-binding proteins (PEBP): a study of the acylpeptide hydrolase and the PEBP inhibitor from the archaeon Sulfolobus solfataricusQ57599845
Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulationsQ57905875
Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidaseQ63214341
Ligand binding affinity prediction by linear interaction energy methodsQ74505232
Validation and use of the MM-PBSA approach for drug discoveryQ81826120
Catalysis of serine oligopeptidases is controlled by a gating filter mechanismQ24522484
Molecular dynamics simulations of DNA-free and DNA-bound TAL effectorsQ27304950
The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller foldQ27640727
Structure and Catalysis of Acylaminoacyl Peptidase: CLOSED AND OPEN SUBUNITS OF A DIMER OLIGOPEPTIDASEQ27665946
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingQ27860652
The Amber biomolecular simulation programsQ27860745
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactionsQ27861128
The gene from the short arm of chromosome 3, at D3F15S2, frequently deleted in renal cell carcinoma, encodes acylpeptide hydrolaseQ28617640
Systematic validation of protein force fields against experimental dataQ28731830
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum modelsQ29616389
Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigationQ31060831
Calculation of absolute protein-ligand binding free energy from computer simulationsQ33784404
Computational study on substrate specificity of a novel cysteine protease 1 precursor from Zea maysQ33907793
Escaping free-energy minimaQ34151010
Families of serine peptidases.Q34317798
Docking validation resources: protein family and ligand flexibility experimentsQ34680415
Prolyl peptidases: a serine protease subfamily with high potential for drug discovery.Q35206949
Catabolism of intracellular N-terminal acetylated proteins: involvement of acylpeptide hydrolase and acylaseQ36145998
Structure-function properties of prolyl oligopeptidase family enzymesQ36470518
Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamicsQ36494755
Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding.Q36546322
Prolyl endopeptidasesQ36679376
Computations of standard binding free energies with molecular dynamics simulationsQ37335295
Evaluation of DOCK 6 as a pose generation and database enrichment toolQ37518530
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Deficiency of acylpeptide hydrolase in small-cell lung carcinoma cell linesQ41602118
Multilevel Parallelization of AutoDock 4.2.Q42080735
How robust are protein folding simulations with respect to force field parameterization?Q42853031
Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1.Q43016205
Alteration of substrate specificities of thermophilic α/β hydrolases through domain swapping and domain interface optimizationQ43016806
Expression, purification and crystal structure of a truncated acylpeptide hydrolase from Aeropyrum pernix K1.Q43018100
Identification of acylpeptide hydrolase as a sensitive site for reaction with organophosphorus compounds and a potential target for cognitive enhancing drugs.Q43506308
Glu88 in the non-catalytic domain of acylpeptide hydrolase plays dual roles: charge neutralization for enzymatic activity and formation of salt bridge for thermodynamic stabilityQ46309931
Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.Q46560922
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)6217-6234
P577publication date2015-03-18
P1433published inInternational Journal of Molecular SciencesQ3153277
P1476titleMolecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos
P478volume16

Reverse relations

cites work (P2860)
Q40153585Exploration of binding and inhibition mechanism of a small molecule inhibitor of influenza virus H1N1 hemagglutinin by molecular dynamics simulation
Q59799699Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations
Q30396469Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations
Q47254850Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations

Search more.