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An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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Improved protein–ligand docking using GOLD

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An improved adaptive genetic algorithm for protein–ligand docking

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Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

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

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Towards the synthesis of bisubstrate inhibitors of protein farnesyltransferase: Synthesis and biological evaluation of new farnesylpyrophosphate analogues

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Reverse hydroxamate-based selective TACE inhibitors

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Discovery of novel hydantoins as selective non-hydroxamate inhibitors of tumor necrosis factor-α converting enzyme (TACE)

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Molecular modelling for transition metal complexes: Dealing with d-electron effects

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Design and synthesis of novel isoxazole-based HDAC inhibitors

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Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs)

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Angiotensin-I-converting enzyme inhibitory peptides: Chemical feature based pharmacophore generation

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Carbonic anhydrase inhibitors. Synthesis, molecular structures, and inhibition of the human cytosolic isozymes I and II and transmembrane isozymes IX, XII (cancer-associated) and XIV with novel 3-pyridinesulfonamide derivatives

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Metal–ligand interactions: An analysis of zinc binding groups using the Protein Data Bank

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An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes

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Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction

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Automatic Selection of Optimal Savitzky−Golay Smoothing

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Finding a Needle in the Haystack: Computational Modeling of Mg2+ Binding in the Active Site of Protein Farnesyltransferase

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Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery

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PEARLS: Program for Energetic Analysis of Receptor−Ligand System

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Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions

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Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?

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Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions

inferredcites →https://doi.org/10.1021/ci500209eopenalex-snapshot

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

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Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function

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GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci700224eopenalex-snapshot

Distance Dependent Scoring Function for Describing Protein−Ligand Intermolecular Interactions

inferredcites →https://doi.org/10.1021/ci7004669openalex-snapshot

AIScore — Chemically Diverse Empirical Scoring Function Employing Quantum Chemical Binding Energies of Hydrogen-Bonded Complexes

inferredcites →https://doi.org/10.1021/ci7004719openalex-snapshot

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA

inferredcites →https://doi.org/10.1021/ci800166popenalex-snapshot

Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot

Comparative Assessment of Scoring Functions on a Diverse Test Set

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Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/ct100091jopenalex-snapshot

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

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Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

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A Transferable Nonbonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

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Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems

inferredcites →https://doi.org/10.1021/ja00022a010openalex-snapshot

Force field design for metalloproteins

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A new force field for modeling metalloproteins

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Simulations of Allosteric Motions in the Zinc Sensor CzrA

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Calculation and Prediction of Binding Free Energies for the Matrix Metalloproteinases

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot

The PDBbind Database: Methodologies and Updates

inferredcites →https://doi.org/10.1021/jm050038sopenalex-snapshot

PMF Scoring Revisited

inferredcites →https://doi.org/10.1021/jm050476zopenalex-snapshot

Metal-Mediated Inhibition of Escherichia coli Methionine Aminopeptidase: Structure−Activity Relationships and Development of a Novel Scoring Function for Metal−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot

A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

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Electrostatic Polarization Is Crucial in Reproducing Cu(I) Interaction Energies and Hydration

inferredcites →https://doi.org/10.1021/pr050361jopenalex-snapshot

Counting the Zinc-Proteins Encoded in the Human Genome

inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

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Announcing the worldwide Protein Data Bank

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On the treatment of electrostatic interactions in biomolecular simulation

inferredcites →https://doi.org/10.1073/pnas.0307578101openalex-snapshot

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

inferredcites →https://doi.org/10.1093/nar/gkh785openalex-snapshot

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

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AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.1093/nar/gkr366openalex-snapshot

SwissDock, a protein-small molecule docking web service based on EADock DSS

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Determination of the interaction potential from the pair distribution function: An inverse Monte Carlo technique

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A fast and elitist multiobjective genetic algorithm: NSGA-II

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The NEOS Server

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PDTD: a web-accessible protein database for drug target identification

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Metalloprotein-Targeted Inhibitors: A Promising Strategy for Novel Pesticide Discovery

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Unlocking Precision Docking for Metalloproteins

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An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design

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Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined

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MetalloDock: Decoding Metalloprotein–Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery

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Metal–ligand interactions in drug design

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Hybrid quantum/classical docking of covalent and non-covalent ligands with Attracting Cavities

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Quantum-machine-assisted drug discovery

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The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins

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MetalProGNet: a structure-based deep graph model for metalloprotein–ligand interaction predictions

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GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability

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GM-DockZn: a geometry matching-based docking algorithm for zinc proteins

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AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 Inhibitors

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Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies

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Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites

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