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Computational protocol for predicting the binding affinities of zinc containing metalloprotein–ligand complexes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Modeling of inhibitor–metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
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Development and testing of a general amber force field
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PM3‐compatible zinc parameters optimized for metalloenzyme active sites
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An empirical potential function for metal centers: Application to molecular mechanics calculations on metalloproteins
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General atomic and molecular electronic structure system
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Analysis of zinc binding sites in protein crystal structures
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
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Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion
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Zinc binding in proteins and solution: A simple but accurate nonbonded representation
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Modeling zinc sulfhydryl bonds in zinc fingers
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Empirical Scale of Side-Chain Conformational Entropy in Protein Folding
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Novel Zinc Protein Molecular Dynamics Simulations: Steps Toward Antiangiogenesis for Cancer Treatment
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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
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Dynamical structure of carboxypeptidase A
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The biological chemistry of the elements
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The biological chemistry of the elements
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An all atom energy based computational protocol for predicting binding affinities of protein–ligand complexes
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A practical approach to docking of zinc metalloproteinase inhibitors
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Automatic atom type and bond type perception in molecular mechanical calculations
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Free Energy Calculations and Ligand Binding
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Carboxypeptidase A: A Protein and an Enzyme
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Statistical potentials and scoring functions applied to protein–ligand binding
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Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction
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Molecular dynamics simulations of metalloproteins
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Structural basis of the action of thermolysin and related zinc peptidases
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Ligand Binding Affinities from MD Simulations
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Carbonic Anhydrase: Evolution of the Zinc Binding Site by Nature and by Design
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Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies
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Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins
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Reevaluation of the Born model of ion hydration
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Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution
inferredcites →https://doi.org/10.1021/ja00022a010openalex-snapshot
Force field design for metalloproteins
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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A new force field for modeling metalloproteins
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A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
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Factors Governing the Protonation State of Zn-Bound Histidine in Proteins: A DFT/CDM Study
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Zn Protein Simulations Including Charge Transfer and Local Polarization Effects
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The Role of Polarization and Charge Transfer in the Solvation of Biomolecules
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Calculation and Prediction of Binding Free Energies for the Matrix Metalloproteinases
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Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm000467kopenalex-snapshot
Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
inferredcites →https://doi.org/10.1021/jm010175zopenalex-snapshot
Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease−Inhibitor Binding
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm030570kopenalex-snapshot
A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm048973nopenalex-snapshot
Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm049050vopenalex-snapshot
A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands
inferredcites →https://doi.org/10.1021/jm980577fopenalex-snapshot
Binding Preferences of Hydroxamate Inhibitors of the Matrix Metalloproteinase Human Fibroblast Collagenase
inferredcites →https://doi.org/10.1021/jp0044476openalex-snapshot
Binding Affinities for a Series of Selective Inhibitors of Gelatinase-A Using Molecular Dynamics with a Linear Interaction Energy Approach
inferredcites →https://doi.org/10.1021/jp004602gopenalex-snapshot
Metal Selectivity in Metalloproteins: Zn2+ vs Mg2+
inferredcites →https://doi.org/10.1021/jp9813692openalex-snapshot
Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments
inferredcites →https://doi.org/10.1023/a:1025386326946openalex-snapshot
Rational selection of training and test sets for the development of validated QSAR models
inferredcites →https://doi.org/10.1038/319199a0openalex-snapshot
Solvation energy in protein folding and binding
inferredcites →https://doi.org/10.1038/nrc884openalex-snapshot
Strategies for MMP inhibition in cancer: innovations for the post-trial era
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1039/fd9929300047openalex-snapshot
Functional zinc-binding motifs in enzymes and DNA-binding proteins
inferredcites →https://doi.org/10.1073/pnas.70.8.2439openalex-snapshot
Structure of Liver Alcohol Dehydrogenase at 2.9-Å Resolution
inferredcites →https://doi.org/10.1073/pnas.87.15.5648openalex-snapshot
Where metal ions bind in proteins.
inferredcites →https://doi.org/10.1093/bioinformatics/btg243openalex-snapshot
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
inferredcites →https://doi.org/10.1093/nar/gkj039openalex-snapshot
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
inferredcites →https://doi.org/10.1093/protein/8.2.127openalex-snapshot
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
inferredcites →https://doi.org/10.1126/science.257.5073.1073openalex-snapshot
The Origin of Plagues: Old and New
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1146/annurev.biophys.30.1.211openalex-snapshot
Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.2174/1381612053382115openalex-snapshot
Recent Developments in the Design of Specific Matrix Metalloproteinase Inhibitors aided by Structural and Computational Studies
inferredcites →https://doi.org/10.2174/1567269053202688openalex-snapshot
A Binding Affinity Based Computational Pathway for Active-Site Directed Lead Molecule Design: Some Promises and Perspectives
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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