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JCIM & JCTC Journals @JCIM_JCTC

1h

Constrained Low-Dimensional Parametrization of Coarse-Grained Force Fields for Structural and Thermodynamic Consistency pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #compchem

Constrained Low-Dimensional Parametrization of Coarse-Grained Force Fields for Structural and...

For complex multicomponent condensed-phase systems, coarse-grained (CG) molecular dynamics often struggles to simultaneously achieve structural fidelity and thermodynamic consistency. Using base...

pubs.acs.org

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Emma Chan , PhD retweeted

JCIM & JCTC Journals @JCIM_JCTC

Jul 4

Efficient and Precise Force Field Optimization for Biomolecules Using DPA-3 pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #ChemicalInformation

Efficient and Precise Force Field Optimization for Biomolecules Using DPA-3

Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However,...

pubs.acs.org

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1,820

Chidambara .ML. retweeted

JCIM & JCTC Journals @JCIM_JCTC

17h

B–Z DNA Transitions under Z–DNA-Favoring Conditions: Benchmarking the OL21-vdW7 Force Field pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #compchem

B–Z DNA Transitions under Z–DNA-Favoring Conditions: Benchmarking the OL21-vdW7 Force Field

The B–Z DNA transition provides a rigorous benchmark for all-atom DNA force fields because it arises from a finely balanced free-energy competition between conformational states with distinct...

pubs.acs.org

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JCIM & JCTC Journals @JCIM_JCTC

21h

Fast Fourier Transform Enables Automated Parametrization of Complex Dihedral Potentials in All-Atom and Coarse-Grained Force Fields pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #compchem

Fast Fourier Transform Enables Automated Parametrization of Complex Dihedral Potentials in All-Atom...

Torsional parametrization remains one of the most persistent challenges and weaknesses of modern force fields, particularly for dihedrals whose asymmetry and multimodality evade traditional Fourier...

pubs.acs.org

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JCIM & JCTC Journals @JCIM_JCTC

Jul 5

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #compchem

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using...

Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods,...

pubs.acs.org

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3,783

Emma Chan , PhD retweeted

JCIM & JCTC Journals @JCIM_JCTC

Jul 3

MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #ChemicalInformation

MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change

Predicting ligand binding free energy change by chemical substitutions is a critical task in drug optimization studies. Despite many efforts, existing computational methods show limited prediction...

pubs.acs.org

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JCIM & JCTC Journals @JCIM_JCTC

Jul 4

Overcoming Shortcut Learning in RNA-Small Molecule Modeling via Bias-Matched Decoys and Structure-Aware Network Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #ChemicalInformation

Overcoming Shortcut Learning in RNA-Small Molecule Modeling via Bias-Matched Decoys and Structure...

Targeting RNA with small molecules represents a promising frontier in drug discovery, yet current computational models are often hindered by the physicochemical property misalignment within available...

pubs.acs.org

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1,063

Chidambara .ML. retweeted

JCIM & JCTC Journals @JCIM_JCTC

Jul 4

3DOpt: Benchmark for Automated Design of 3D Molecular Structures across the Periodic Table pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #ChemicalInformation

3DOpt: Benchmark for Automated Design of 3D Molecular Structures across the Periodic Table

The automated design of three-dimensional (3D) molecular structures is a rapidly advancing field with major applications in drug discovery, catalysis, and materials science. Despite this progress,...

pubs.acs.org

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Chidambara .ML. retweeted

JCIM & JCTC Journals @JCIM_JCTC

Jul 3

Toward Lab-Ready AI Synthesis Plans with Protection Strategies and Route Scoring pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue11 #MachineLearning #DeepLearning

Toward Lab-Ready AI Synthesis Plans with Protection Strategies and Route Scoring

AI-driven synthesis planning tools are developed to automatically create synthesis routes and thereby aid chemists in making novel molecules. However, these tools frequently produce reaction trees...

pubs.acs.org

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