47 results on '"MacKerell, Alexander"'
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2. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation
3. Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins
4. Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes
5. Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids
6. Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES–Fatty Acid Micellar System
7. Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?
8. Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155–4
9. Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor
10. Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model
11. Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides
12. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields
13. CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides
14. Competition among Li+, Na+, K+, and Rb+Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields
15. Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution
16. Perturbation of Long-Range Water Dynamics as the Mechanism for the Antifreeze Activity of Antifreeze Glycoprotein
17. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
18. Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments
19. Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
20. A Comparative Kirkwood-Buff Study of Aqueous Methanol Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields
21. A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
22. Molecular Details of the Activation of the μ Opioid Receptor
23. Bifurcated Hydrogen Bonding and Asymmetric Fluctuations in a Carbohydrate Crystal Studied via X-ray Crystallography and Computational Analysis
24. Comprehensive Conformational Studies of Five Tripeptides and a Deduced Method for Efficient Determinations of Peptide Structures
25. Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides
26. Consensus 3D Model of μ-Opioid Receptor Ligand Efficacy Based on a Quantitative Conformationally Sampled Pharmacophore
27. Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters
28. Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model
29. Conformational Properties of Methyl β-Maltoside and Methyl α- and β-Cellobioside Disaccharides
30. CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses
31. Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling
32. Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at the Water/Air Interface
33. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
34. CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose
35. Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field
36. Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids: A Molecular Dynamics Study
37. Direct Comparisons of Experimental and Calculated Neutron Structure Factors of Pure Solvents as a Method for Force Field Validation
38. Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator
39. Conserved Patterns in Backbone Torsional Changes Allow for Single Base Flipping from Duplex DNA with Minimal Distortion of the Double Helix
40. Development of an Empirical Force Field for Silica. Application to the Quartz−Water Interface
41. Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model
42. An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer
43. Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations
44. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
45. Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics
46. Conformational Properties of the Deoxyribose and Ribose Moieties of Nucleic Acids: A Quantum Mechanical Study
47. Influence of Magnesium Ions on Duplex DNA Structural, Dynamic, and Solvation Properties
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