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Journal of Chemical Theory and Computation

https://doi.org/10.1021/issn.1549-9618
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Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00451openalex-snapshot
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00575openalex-snapshot
SARS-CoV‑2 Main Protease: A Molecular Dynamics Study
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00687openalex-snapshot
Deep Learning Total Energies and Orbital Energies of Large Organic Molecules Using Hybridization of Molecular Fingerprints
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00698openalex-snapshot
Prediction of Molecular Electronic Transitions Using Random Forests
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00699openalex-snapshot
Thermochemical Data Fusion Using Graph Representation Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01010openalex-snapshot
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01041openalex-snapshot
tmQM Dataset─Quantum Geometries and Properties of 86k Transition Metal Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01203openalex-snapshot
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01224openalex-snapshot
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01329openalex-snapshot
A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01424openalex-snapshot
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00029openalex-snapshot
Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00203openalex-snapshot
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00256openalex-snapshot
DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00447openalex-snapshot
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00560openalex-snapshot
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00655openalex-snapshot
Molecular Environment-Specific Atomic Charges Improve Binding Affinity Predictions of SAMPL5 Host–Guest Systems
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00924openalex-snapshot
Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00998openalex-snapshot
Making it Rain: Cloud-Based Molecular Simulations for Everyone
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01346openalex-snapshot
TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01424openalex-snapshot
EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01497openalex-snapshot
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01523openalex-snapshot
SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00201openalex-snapshot
Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00234openalex-snapshot
Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00483openalex-snapshot
Capturing the Recognition Dynamics of para -Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00616openalex-snapshot
Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00760openalex-snapshot
Cheap Turns Superior: A Linear Regression-Based Correction Method to Reaction Energy from the DFT
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00945openalex-snapshot
LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01184openalex-snapshot
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01235openalex-snapshot
ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01296openalex-snapshot
BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01448openalex-snapshot
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01505openalex-snapshot
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00557openalex-snapshot
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00660openalex-snapshot
HiREX: High-Throughput Reactivity Exploration for Extended Databases of Transition-Metal Catalysts
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00772openalex-snapshot
Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00948openalex-snapshot
Pynta─An Automated Workflow for Calculation of Surface and Gas–Surface Kinetics
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01049openalex-snapshot
AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01245openalex-snapshot
Conformer Generation for Structure-Based Drug Design: How Many and How Good?
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01278openalex-snapshot
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01313openalex-snapshot
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01513openalex-snapshot
Polarizable AMOEBA Model for Simulating Mg 2+ ·Protein·Nucleotide Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01691openalex-snapshot
Parameterization of General Organic Polymers within the Open Force Field Framework
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01864openalex-snapshot
Deconvolution and Analysis of the 1 H NMR Spectra of Crude Reaction Mixtures
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00055openalex-snapshot
Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00339openalex-snapshot
Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00417openalex-snapshot
Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00442openalex-snapshot
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00475openalex-snapshot
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00833openalex-snapshot
Covalent Adducts Formed by the Androgen Receptor Transactivation Domain and Small Molecule Drugs Remain Disordered
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01298openalex-snapshot
Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01355openalex-snapshot
Transferable Neural Network Potentials and Condensed Phase Properties
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02179openalex-snapshot
Cluster-Graph Fingerprinting: A Framework for Quantitative Analysis of Machine-Learned Interatomic Model Training and Simulation Data
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00646openalex-snapshot
Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00904openalex-snapshot
The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00301openalex-snapshot
Multicriteria Optimization of Molecular Models of Water Using a Reduced Units Approach
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