219 results on '"Geerke, Daan P."'
Search Results
2. OFraMP: a fragment-based tool to facilitate the parametrization of large molecules
3. Polarisable force fields: What do they add in biomolecular simulations?
4. ELIXIR and Toxicology: a community in development
5. A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants
6. Engineering a self-sufficient Mycobacterium tuberculosis CYP130 by gene fusion with the reductase-domain of CYP102A1 from Bacillus megaterium
7. Distant sequence regions of JBP1 contribute to J-DNA binding
8. Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach
9. Distant sequence regions of JBP1 contribute to J-DNA binding.
10. An efficient, site‐selective and spontaneous peptide macrocyclisation during in vitro translation
11. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2
12. Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs
13. Charge Group Partitioning in Biomolecular Simulation
14. Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex
15. Genetic Control and Evolution of Anthocyanin Methylation
16. Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions
17. C−X Bond Activation by Palladium: Steric Shielding versus Steric Attraction
18. An Efficient, Site‐Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation.
19. An anti-tuberculosis compound screen using a zebrafish infection model identifies an aspartyl-tRNA synthetase inhibitor
20. ELIXIR and Toxicology: a community in development
21. Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations
22. Polarisable force fields: what do they add in biomolecular simulations?
23. A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450‐Catalyzed Substrate Conversion
24. Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration
25. Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation
26. DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals
27. A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation
28. Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol
29. Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model
30. Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane
31. Enhancing protein-drug binding prediction
32. Abstract 5861: RX-3117 promotes epigenetic effects in cancer cells through enhanced degradation of DNMT1
33. eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations
34. Comprehensive and automated Linear Interaction Energy based binding-affinity prediction applied to Cytochrome P450 aromatase inhibitors
35. Calculation of the free energy of polarization: Quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters
36. Enumerating common molecular substructures
37. Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors
38. Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors
39. A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols
40. An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures
41. Combined Simulation and Mutation Studies to Elucidate Selectivity of Unsubstituted Amphetamine-like Cathinones at the Dopamine Transporter
42. To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures
43. Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations
44. Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation
45. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.
46. Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project
47. ORGN 211-The effect of steric bulk on Pd, PdCl- and Pd(PH3)(2) catalyzed C-C bond activation: Perspectives from an extended activation strain model
48. Combined Simulation and Mutation Studies to Elucidate Selectivity of Unsubstituted Amphetamine-like Cathinones at the Dopamine Transporter.
49. Mutation in KERA Identified by Linkage Analysis and Targeted Resequencing in a Pedigree with Premature Atherosclerosis
50. A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities
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