184 results on '"Merz Jr., Kenneth M."'
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2. Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.
3. End-to-End Differentiable Reactive Molecular Dynamics Simulations Using JAX
4. Getting zinc into and out of cells
5. LigandDiff: 3D Transition Metal Complex Generation with Diffusion Models
6. LigandDiff: de Novo Ligand Design for 3D Transition Metal Complexes with Diffusion Models.
7. Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution.
8. Molecular Gas Phase Conformational Ensembles
9. Modeling Fe(II) Complexes Using Neural Networks.
10. Molecular Gas-Phase Conformational Ensembles.
11. Thermodynamics of Metal–Acetate Interactions.
12. Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers.
13. Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge
14. Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input.
15. QM/MM Simulations on NVIDIA and AMD GPUs
16. JAX-ReaxFF: Gradient-Based Framework for Fast Optimization of Reactive Force Fields
17. Consequences of Overfitting the van der Waals Radii of Ions.
18. Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units.
19. A Polarizable Cationic Dummy Metal Ion Model
20. JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields
21. Accurate Metal–Imidazole Interactions.
22. AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.
23. Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications.
24. JAX-ReaxFF: A Gradient-Based Framework for Fast Optimization of Reactive Force Fields.
25. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods
26. JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields
27. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores
28. Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV‑2.
29. A Polarizable Cationic Dummy Metal Ion Model.
30. Systematic Evaluation of Ion Diffusion and Water Exchange.
31. Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK
32. Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program
33. The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.
34. Can we separate active from inactive conformations?
35. Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program
36. Parallel implementation of a divide and conquer semiempirical algorithm
37. The application of the genetic algorithm to the minimization of potential energy functions
38. Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.
39. Validation of AMBER/GAFF for Relative Free Energy Calculations
40. AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations.
41. Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.
42. ReaxFF/AMBERA Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations.
43. Evolution of Alchemical Free Energy Methods in Drug Discovery.
44. Validation of Free Energy Methods in AMBER.
45. MRP.py: A Parametrizer of Post-Translationally Modified Residues.
46. Receptor–Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method.
47. Pair Potentials as Machine Learning Features.
48. Metabolite Structure Assignment Using In Silico NMR Techniques.
49. Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program.
50. Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.
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