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  1. Discovery and Preliminary Characterization of Lactose-Transforming Enzymes in Ewingella americana L47: A Genomic, Biochemical, and In Silico Approach

    Article • International Journal of Molecular Sciences, January 2026, MDPI AG

    Dr Jans H. Alzate-Morales

  2. Molecular Insights into Phosphonium-Based Ionic Liquid Extraction of Phenolic Pollutants from Aqueous Solutions

    Article • The Journal of Physical Chemistry B, July 2025, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  3. Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods

    Article • Journal of Chemical Information and Modeling, May 2025, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  4. Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations

    Article • ACS Omega, April 2025, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  5. Computational Study of the 1,3-Dipolar Cycloaddition between Criegee Intermediates and Linalool: Atmospheric Implications

    Article • The Journal of Physical Chemistry A, January 2025, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  6. Understanding the Differences of Danusertib’s Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations

    Article • Journal of Chemical Information and Modeling, June 2024, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  7. Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition

    Article • Journal of Chemical Information and Modeling, May 2024, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  8. Front Cover: Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations. (ChemCatChem 17/2023)

    Article • ChemCatChem, August 2023, Wiley

    Dr Jans H. Alzate-Morales

  9. Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations.

    Article • ChemCatChem, July 2023, Wiley

    Dr Jans H. Alzate-Morales

  10. Can graphene improve the thermal conductivity of copper nanofluids?

    Article • Physical Chemistry Chemical Physics, January 2023, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  11. Effect of strand register in the stability and reactivity of crystals from peptides forming amyloid fibrils

    Article • Physical Chemistry Chemical Physics, January 2023, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  12. Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa

    Article • Journal of Chemical Information and Modeling, June 2022, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  13. Understanding the differences of Danusertib’s Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified Using Conventional and Enhanced Molecular Dynamics Simulations.

    Article • May 2022, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  14. Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP‐dependent vitamin kinase family members

    Article • Protein Science, February 2021, Wiley

    Dr Jans H. Alzate-Morales

  15. How a Second Mg2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study

    Article • ACS Catalysis, December 2020, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  16. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field

    Article • Journal of Chemical Information and Modeling, July 2020, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  17. How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

    Article • July 2020, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  18. Characterization of hydroxymethylpyrimidine phosphate kinase from mesophilic and thermophilic bacteria and structural insights into their differential thermal stability

    Article • Archives of Biochemistry and Biophysics, July 2020, Elsevier

    Dr Jans H. Alzate-Morales

  19. Parameterization of Divalent Cations for Coarse-Grained Simulations

    Article • February 2020, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  20. Tetrahydroquinoline-Isoxazole/Isoxazoline Hybrid Compounds as Potential Cholinesterases Inhibitors: Synthesis, Enzyme Inhibition Assays, and Molecular Modeling Studies

    Article • International Journal of Molecular Sciences, December 2019, MDPI AG

    Dr Jans H. Alzate-Morales

  21. Molecular Insights into the Trapping Effect of Ca2+ in Protein Kinase A: A Molecular Dynamics Study

    Article • Journal of Chemical Information and Modeling, December 2019, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  22. Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study

    Article • PLOS One, September 2019, PLOS

    Dr Jans H. Alzate-Morales

  23. Experimental and Theoretical Approaches in the Study of Phenanthroline‐Tetrahydroquinolines for Alzheimer's Disease

    Article • ChemistryOpen, May 2019, Wiley

    Dr Jans H. Alzate-Morales

  24. Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr Jans H. Alzate-Morales

  25. Classical and Quantum Mechanical Calculations of the Stacking Interaction of NdIII Complexes with Regular and Mismatched DNA Sequences

    Article • The Journal of Physical Chemistry B, March 2019, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  26. Assessing the effect of calcium and magnesium ions in the structural stability of the protein kinase A through molecular dynamics simulations

    Article • January 2019, MDPI AG

    Dr Jans H. Alzate-Morales

  27. Novel Coumarin-Quinoline Hybrids: Design of Multitarget Compounds for Alzheimer's Disease

    Article • ChemistrySelect, January 2019, Wiley

    Dr Maria João Matos, Dr Jans H. Alzate-Morales

  28. Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study

    Article • Computational and Structural Biotechnology Journal, January 2019, Elsevier

    Dr Jans H. Alzate-Morales

  29. Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations

    Article • Chemical Science, January 2019, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  30. Inhibition of key enzymes in the inflammatory pathway by hybrid molecules of terpenes and synthetic drugs: In vitro and in silico studies

    Article • Chemical Biology & Drug Design, October 2018, Wiley

    Dr Guillermo Schmeda-Hirschmann, Dr Jans H. Alzate-Morales

  31. Folding and Lipid Composition Determine Membrane Interaction of the Disordered Protein COR15A

    Article • Biophysical Journal, September 2018, Elsevier

    Dr Jans H. Alzate-Morales

  32. Design, facile synthesis, and evaluation of novel spiro- and pyrazolo[1,5- c ]quinazolines as cholinesterase inhibitors: Molecular docking and MM/GBSA studies

    Article • Computational Biology and Chemistry, June 2018, Elsevier

    Dr Jans H. Alzate-Morales

  33. Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition

    Article • Biochemistry, May 2018, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  34. Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

    Article • March 2018, IntechOpen

    Dr Jans H. Alzate-Morales

  35. On the Reaction Mechanism of the 3,4-Dimethoxybenzaldehyde Formation from 1-(3′,4′-Dimethoxyphenyl)Propene

    Article • Molecules, February 2018, MDPI AG

    Dr Jans H. Alzate-Morales

  36. Computational Studies of Snake Venom Toxins

    Article • Toxins, December 2017, MDPI AG

    Dr Jans H. Alzate-Morales

  37. Combined molecular modelling and 3D-QSAR study for understanding the inhibition of NQO1 by heterocyclic quinone derivatives

    Article • Chemical Biology & Drug Design, August 2017, Wiley

    Dr Jans H. Alzate-Morales, Cristian Salas

  38. Modeling cooperative effects in halogen-bonded infinite linear chains

    Article • Physical Chemistry Chemical Physics, January 2017, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  39. Ruthenium(ii) complexes incorporating carbazole–diazafluorene based bipolar ligands for dye sensitized solar cell applications

    Article • New Journal of Chemistry, January 2017, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  40. Molecular dynamics analysis of the binding mechanism of veratryl alcohol at the protein surface of lignin peroxidase (P. chrysosporium) and its mutants E168Q and D264N.

    Article • November 2016, MDPI AG

    Dr Jans H. Alzate-Morales

  41. Insights into the inhibitory effect of Ca2+ on protein kinase A from molecular dynamics simulations.

    Article • November 2016, MDPI AG

    Dr Jans H. Alzate-Morales

  42. Novel N ‐allyl/propargyl tetrahydroquinolines: Synthesis via Three‐component Cationic Imino Diels–Alder Reaction, Binding Prediction, and Evaluation as Cholinesterase Inhibitors

    Article • Chemical Biology & Drug Design, June 2016, Wiley

    Dr Jans H. Alzate-Morales

  43. Structural and Affinity Determinants in the Interaction between Alcohol Acyltransferase from F. x ananassa and Several Alcohol Substrates: A Computational Study

    Article • PLOS One, April 2016, PLOS

    Dr Jans H. Alzate-Morales

  44. Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches

    Article • Theoretical Chemistry Accounts, March 2016, Springer Science + Business Media

    Dr Jans H. Alzate-Morales

  45. Synthesis and in silico analysis of the quantitative structure–activity relationship of heteroaryl–acrylonitriles as AChE inhibitors

    Article • Journal of the Taiwan Institute of Chemical Engineers, February 2016, Elsevier

    Dr Jans H. Alzate-Morales

  46. Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  47. Halogen bonding in drug-like molecules: a computational and systematic study of the substituent effect

    Article • RSC Advances, January 2016, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  48. Multiple binding sites in the nicotinic acetylcholine receptors: An opportunity for polypharmacolgy

    Article • Pharmacological Research, November 2015, Elsevier

    Dr Jans H. Alzate-Morales

  49. A characterization of the two-step reaction mechanism of phenol decomposition by a Fenton reaction

    Article • Chemical Physics Letters, November 2015, Elsevier

    Dr Jans H. Alzate-Morales

  50. Similarities between the Binding Sites of SB-206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile

    Article • PLOS One, August 2015, PLOS

    Dr Jans H. Alzate-Morales

  51. Computational study of the complexation of metals ions with poly(amidoamine) PAMAM G0 dendrimers

    Article • Chemical Physics Letters, November 2014, Elsevier

    Dr Jans H. Alzate-Morales

  52. Ultrasound-assisted phase-transfer catalysis method in an aqueous medium to promote the Knoevenagel reaction: Advantages over the conventional and microwave-assisted solvent-free/catalyst-free method

    Article • Ultrasonics Sonochemistry, September 2014, Elsevier

    Dr Jans H. Alzate-Morales

  53. Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case

    Article • Physical Chemistry Chemical Physics, January 2014, Royal Society of Chemistry

    Dr Jans H. Alzate-Morales

  54. Synthesis of Bistetrahydroquinolines as Potential Anticholinesterasic Agents by Double Diels-Alder Reactions

    Article • Molecules, October 2013, MDPI AG

    Dr Jans H. Alzate-Morales

  55. Neonicotinic analogues: Selective antagonists for α4β2 nicotinic acetylcholine receptors

    Article • Bioorganic & Medicinal Chemistry, May 2013, Elsevier

    Dr Jans H. Alzate-Morales

  56. Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations

    Article • Journal of Molecular Graphics and Modelling, February 2013, Elsevier

    Dr Jans H. Alzate-Morales

  57. Synthesis, in silico, in vitro, and in vivo investigation of 5-[11C]methoxy-substituted sunitinib, a tyrosine kinase inhibitor of VEGFR-2

    Article • European Journal of Medicinal Chemistry, December 2012, Elsevier

    Dr Jans H. Alzate-Morales

  58. A Novel Class of Selective Acetylcholinesterase Inhibitors: Synthesis and Evaluation of (E)-2-(Benzo[d]thiazol-2-yl)-3-heteroarylacrylonitriles

    Article • Molecules, October 2012, MDPI AG

    Dr Jans H. Alzate-Morales

  59. Molecular Dynamics of Protein Kinase-Inhibitor Complexes: A Valid Structural Information

    Article • Current Pharmaceutical Design, May 2012, Bentham Science Publishers

    Dr Jans H. Alzate-Morales

  60. The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids

    Article • Biochemical Journal, February 2012, Portland Press Ltd.

    Dr Jans H. Alzate-Morales

  61. Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations

    Article • Journal of Molecular Graphics and Modelling, February 2012, Elsevier

    Dr Jans H. Alzate-Morales

  62. Synthesis of the Indolo[2,3-a]quinolizidine Ring through the Addition of 2-Siloxyfurans to Imines and Intrinsic Reaction Coordinate Calculations

    Article • Synthesis, December 2011, Thieme Publishing Group

    Dr Jans H. Alzate-Morales

  63. Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-BasedDe NovoDesign: Study of Binding Mode of Diastereomer...

    Article • Journal of Chemical Information and Modeling, November 2011, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  64. Docking and quantitative structure–activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met k...

    Article • Journal of Computer-Aided Molecular Design, April 2011, Springer Science + Business Media

    Dr Jans H. Alzate-Morales

  65. Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site

    Article • Journal of Chemical Information and Modeling, June 2010, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  66. Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM

    Article • Journal of Chemical Information and Modeling, January 2010, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  67. Selective Interaction of Lansoprazole and Astemizole with Tau Polymers: Potential New Clinical Use in Diagnosis of Alzheimer's Disease

    Article • Journal of Alzheimer’s Disease, January 2010, IOS Press

    Dr Jans H. Alzate-Morales

  68. A computational ONIOM model for the description of the H-bond interactions between NU2058 analogues and CDK2 active site

    Article • Chemical Physics Letters, September 2009, Elsevier

    Dr Jans H. Alzate-Morales

  69. Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations

    Article • Journal of Chemical Information and Modeling, April 2009, American Chemical Society (ACS)

    Dr Jans H. Alzate-Morales

  70. Theoretical Study on CDK2 Inhibitors Using a Global Softness Obtained from the Density of States

    Article • The Journal of Physical Chemistry B, March 2007, American Chemical Society (ACS)

    Dr William Tiznado, Dr Jans H. Alzate-Morales

  71. A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Predictor of the Biological Activity

    Article • Biophysical Journal, January 2007, Elsevier

    Dr Jans H. Alzate-Morales