Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential (Q36059874)

11 August 2017

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential (English)

1 reference

11 August 2017

1 reference

Jiajing Zhang

1

1 reference

11 August 2017

Wei Yang

series ordinal

2

1 reference

11 August 2017

Jean-Philip Piquemal

series ordinal

3

1 reference

11 August 2017

Pengyu Ren

series ordinal

4

1 reference

11 August 2017

2 January 2012

1 reference

Journal of Chemical Theory and Computation

11 August 2017

1 reference

11 August 2017

8

1 reference

11 August 2017

4

1 reference

11 August 2017

1314-1324

1 reference

Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Matrix metalloproteinases as drug targets in ischemia/reperfusion injury.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Pyrone-Based Inhibitors of Metalloproteinase Types 2 and 3 May Work as Conformation-Selective Inhibitors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Multipole electrostatics in hydration free energy calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Molecular simulations of ion channels: a quantum chemist's perspective

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Current status of the AMOEBA polarizable force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Extra binding region induced by non-zinc chelating inhibitors into the S1' subsite of matrix metalloproteinase 8 (MMP-8)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Intracellular zinc homeostasis and zinc signaling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Calculation of protein-ligand binding free energy by using a polarizable potential

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Design of zinc binding functions for carbonic anhydrase inhibitors.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Structural basis for AMP binding to mammalian AMP-activated protein kinase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Matrix metalloproteinase inhibitors as therapy for inflammatory and vascular diseases.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Tuning ion coordination architectures to enable selective partitioning

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Matrix metalloproteinase inhibitors as prospective agents for the prevention and treatment of cardiovascular and neoplastic diseases

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

The Amber biomolecular simulation programs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Highly efficient endogenous human gene correction using designed zinc-finger nucleases

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Structural basis for the highly selective inhibition of MMP-13.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Making a new turn in matrix metalloprotease inhibition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Interaction of viral proteins with metal ions: role in maintaining the structure and functions of viruses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Synthetic analogues relevant to the structure and function of zinc enzymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Binuclear Metallohydrolases

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Structure and dynamics of calmodulin in solution.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

The biochemical basis of zinc physiology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Structural Biology of Zinc

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Metal-binding sites in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable atomic multipole X-ray refinement: application to peptide crystals

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Physical basis of structural and catalytic Zn-binding sites in proteins

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Metal-coupled folding of Cys2His2 zinc-finger.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Molecular dynamics simulations of peptide carboxylate hydration

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Zn protein simulations including charge transfer and local polarization effects

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Binding affinity of hydroxamate inhibitors of matrix metalloproteinase-2.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Ion solvation thermodynamics from simulation with a polarizable force field

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Calculation and prediction of binding free energies for the matrix metalloproteinases

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Modeling of inhibitor-metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383645

Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein

23 September 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Gd(III) Polyaminocarboxylate Chelate: Realistic Many-Body Molecular Dynamics Simulations for Molecular Imaging Applications

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Quasichemical and structural analysis of polarizable anion hydration

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Force Field Modeling of Amino Acid Conformational Energies

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Molecular Dynamics Study of the Hydration of Lanthanum(III) and Europium(III) Including Many-Body Effects

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Polarization and charge transfer in the hydration of chloride ions

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Synthesis of a series of stromelysin-selective thiadiazole urea matrix metalloproteinase inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Recent Advances in Zinc Enzymology

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Structure-based design and synthesis of novel non-zinc chelating MMP-12 inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22754403

12 December 2020

Identifiers

DOI

10.1021/CT200812Y

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22754403

1 reference