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A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase–ligand and FKBP–ligand systemsJournal of Computer-Aided Molecular Design28 dayssaveRefWorksSFX Info
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modelingJournal of Computer-Aided Molecular Design62 dayssaveRefWorksSFX Info
Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulatorsJournal of Computer-Aided Molecular Design70 dayssaveRefWorksSFX Info
Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field methodJournal of Computer-Aided Molecular Design72 dayssaveRefWorksSFX Info
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approachJournal of Computer-Aided Molecular Design72 dayssaveRefWorksSFX Info
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision treeJournal of Computer-Aided Molecular Design73 dayssaveRefWorksSFX Info
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approachJournal of Computer-Aided Molecular Design73 dayssaveRefWorksSFX Info
Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approachJournal of Computer-Aided Molecular Design104 dayssaveRefWorksSFX Info
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challengeJournal of Computer-Aided Molecular Design104 dayssaveRefWorksSFX Info
How N -(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives are arranged in the interlayer space of zirconium sulfophenylphosphonate: a problem solved by experimental and calculation methodsJournal of Computer-Aided Molecular Design106 dayssaveRefWorksSFX Info
Standard state free energies, not pK a s, are ideal for describing small molecule protonation and tautomeric statesJournal of Computer-Aided Molecular Design106 dayssaveRefWorksSFX Info
Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assayJournal of Computer-Aided Molecular Design108 dayssaveRefWorksSFX Info
Drug Design Data Resource, Grand Challenge 4, second of two issuesJournal of Computer-Aided Molecular Design115 dayssaveRefWorksSFX Info
Quantum chemical predictions of water–octanol partition coefficients applied to the SAMPL6 log P blind challengeJournal of Computer-Aided Molecular Design119 dayssaveRefWorksSFX Info
SAMPL6 log P challenge: machine learning and quantum mechanical approachesJournal of Computer-Aided Molecular Design119 dayssaveRefWorksSFX Info
A deep learning approach for the blind logP prediction in SAMPL6 challengeJournal of Computer-Aided Molecular Design119 dayssaveRefWorksSFX Info
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculationsJournal of Computer-Aided Molecular Design122 dayssaveRefWorksSFX Info
The SAMPL6 challenge on predicting octanol–water partition coefficients from EC-RISM theoryJournal of Computer-Aided Molecular Design125 dayssaveRefWorksSFX Info
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energiesJournal of Computer-Aided Molecular Design126 dayssaveRefWorksSFX Info
Conformational analysis of macrocycles: comparing general and specialized methodsJournal of Computer-Aided Molecular Design128 dayssaveRefWorksSFX Info
The role of human in the loop: lessons from D3R challenge 4Journal of Computer-Aided Molecular Design128 dayssaveRefWorksSFX Info
Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity predictionJournal of Computer-Aided Molecular Design129 dayssaveRefWorksSFX Info
Prediction of octanol-water partition coefficients for the SAMPL6- $$\log P$$logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fieldsJournal of Computer-Aided Molecular Design129 dayssaveRefWorksSFX Info
SAMPL6 Octanol–water partition coefficients from alchemical free energy calculations with MBIS atomic chargesJournal of Computer-Aided Molecular Design129 dayssaveRefWorksSFX Info
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fieldsJournal of Computer-Aided Molecular Design129 dayssaveRefWorksSFX Info
Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tractsJournal of Computer-Aided Molecular Design133 dayssaveRefWorksSFX Info
A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approachJournal of Computer-Aided Molecular Design135 dayssaveRefWorksSFX Info
LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge moleculesJournal of Computer-Aided Molecular Design135 dayssaveRefWorksSFX Info
A comparison of molecular representations for lipophilicity quantitative structure–property relationships with results from the SAMPL6 logP Prediction ChallengeJournal of Computer-Aided Molecular Design136 dayssaveRefWorksSFX Info
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Software to obtain spatially localized functions from different radial functionsJournal of Computer-Aided Molecular Design147 dayssaveRefWorksSFX Info
Influence of feature rankers in the construction of molecular activity prediction modelsJournal of Computer-Aided Molecular Design149 dayssaveRefWorksSFX Info
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4Journal of Computer-Aided Molecular Design154 dayssaveRefWorksSFX Info
Octanol–water partition coefficient measurements for the SAMPL6 blind prediction challengeJournal of Computer-Aided Molecular Design160 dayssaveRefWorksSFX Info
A noncanonical binding site of linezolid revealed via molecular dynamics simulationsJournal of Computer-Aided Molecular Design167 dayssaveRefWorksSFX Info
Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2Journal of Computer-Aided Molecular Design169 dayssaveRefWorksSFX Info
Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approachesJournal of Computer-Aided Molecular Design171 dayssaveRefWorksSFX Info
This issue: Drug Design Data Resource Grand Challenge 4, first of two issuesJournal of Computer-Aided Molecular Design178 dayssaveRefWorksSFX Info
Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine LearningJournal of Computer-Aided Molecular Design178 dayssaveRefWorksSFX Info
Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screeningJournal of Computer-Aided Molecular Design178 dayssaveRefWorksSFX Info
Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinomeJournal of Computer-Aided Molecular Design178 dayssaveRefWorksSFX Info
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4Journal of Computer-Aided Molecular Design181 dayssaveRefWorksSFX Info
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitorsJournal of Computer-Aided Molecular Design182 dayssaveRefWorksSFX Info
Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein–protein interactionJournal of Computer-Aided Molecular Design182 dayssaveRefWorksSFX Info
Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energiesJournal of Computer-Aided Molecular Design182 dayssaveRefWorksSFX Info
Prediction of the n -octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculationsJournal of Computer-Aided Molecular Design183 dayssaveRefWorksSFX Info
Undersampling: case studies of flaviviral inhibitory activitiesJournal of Computer-Aided Molecular Design183 dayssaveRefWorksSFX Info
Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidaseJournal of Computer-Aided Molecular Design184 dayssaveRefWorksSFX Info
COSMO-RS based predictions for the SAMPL6 logP challengeJournal of Computer-Aided Molecular Design184 dayssaveRefWorksSFX Info
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