All Stories

  1. Theoretical Insights into MutY Glycosylase DNA Repair Mechanism
  2. A spectroscopic and structural study on the solvent-promoted stereospecific self-assembly of new Porphyrin-Bile Salt conjugates
  3. Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates
  4. A finely balanced order–disorder equilibrium sculpts the folding–binding landscape of an antibiotic sequestering protein
  5. A Theoretical‐Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature
  6. Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution
  7. Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical–Computational Study
  8. ERAP1 and ERAP2 Haplotypes Influence Suboptimal HLA-B*27:05-Restricted Anti-Viral CD8+ T Cell Responses Cross-Reactive to Self-Epitopes
  9. Unveiling the Excited State Dynamics of Indole in Solution
  10. Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis
  11. Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP
  12. A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole
  13. Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense
  14. PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method
  15. Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases
  16. Effects of Environmental and Electric Perturbations on the pKa of Thioredoxin Cysteine 35: A Computational Study
  17. Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs
  18. Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations
  19. Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein
  20. The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States
  21. Theoretical Modeling of Redox Potentials of Biomolecules
  22. Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study
  23. Complexation and organization of doxorubicin on polystyrene sulfonate chains: impacts on doxorubicin dimerization and quenching
  24. Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics
  25. Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States
  26. Modelling the Activation Pathways in Full-Length Src Kinase
  27. Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution
  28. Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches
  29. The full model of the pMHC-TCR-CD3 complex: a structural and kinetics characterization
  30. Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions
  31. Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors
  32. EBV, CD8 and Ankylosing spondylitis
  33. Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins
  34. On the activation and deactivation pathways of the Lck kinase domain: a computational study
  35. Theoretical–computational modelling of the temperature dependence of the folding–unfolding thermodynamics and kinetics: the case of a Trp-cage
  36. Efficient and Accurate Modeling of Conformational Transitions in Proteins: The Case of c-Src Kinase
  37. Understanding the indirect DNA read-out specificity of I-CreI Meganuclease
  38. A Stereochemically Driven Supramolecular Polymerisation
  39. 2-(Hydroxyimino)aldehydes: Photo- and Physicochemical Properties of a Versatile Functional Group for Monomer Design
  40. Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives
  41. Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI
  42. Density discriminates between thermophilic and mesophilic proteins
  43. Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations
  44. Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II)
  45. Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment
  46. Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives
  47. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics
  48. Role of the hydrophilic spacer of glucosylated amphiphiles included in liposome formulations in the recognition of Concanavalin A
  49. The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain
  50. Theoretical calculation of the pyrene emission properties in different solvents
  51. Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold
  52. Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins
  53. In silico characterization of protein partial molecular volumes and hydration shells
  54. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges
  55. Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions
  56. Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution
  57. Molecular mechanisms of activation in CDK2
  58. Molecular dynamics of the full-length p53 monomer
  59. On the Nature of DNA Hyperchromic Effect
  60. Non-specific protein–DNA interactions control I-CreI target binding and cleavage
  61. Conformational Selection versus Induced Fit in Kinases: The Case of PI3K-γ
  62. Effects of local electric fields on the redox free energy of single stranded DNA
  63. Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin
  64. MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
  65. Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data
  66. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
  67. Kinetics of Carbon Monoxide Migration and Binding in Solvated Myoglobin as Revealed by Molecular Dynamics Simulations and Quantum Mechanical Calculations
  68. On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes
  69. Theoretical Characterization of the Dynamical Behavior and Transport Properties of α,γ-Peptide Nanotubes in Solution
  70. FlexServ: an integrated tool for the analysis of protein flexibility
  71. Theoretical characterization of electronic states in interacting chemical systems
  72. Charge transfer equilibria of aqueous single stranded DNA
  73. What can we learn by comparing experimental and theoretical-computational X-ray scattering data?
  74. Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions With Microwave Fields: The Case Study of Myoglobin
  75. Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data
  76. Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state
  77. Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water
  78. Theoretical study of intramolecular charge transfer in π-conjugated oligomers
  79. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin
  80. On the importance of configurational sampling in theoretical calculation of electronic properties of complex molecular systems: Acetone in water
  81. Conformational behavior of temporin A and temporin L in aqueous solution: A computational/experimental study
  82. Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution
  83. Myoglobin as a Case Study for Molecular Simulations in the Presence of a Microwave Electromagnetic Field
  84. Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde
  85. Theoretical Characterization of α-Helix and β-Hairpin Folding Kinetics
  86. Ground and excited electronic state thermodynamics of aqueous carbon monoxide: A theoretical study
  87. Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case
  88. Characterization of liquid behaviour by means of local density fluctuations
  89. Calculation of the optical rotatory dispersion of solvated alanine by means of the perturbed matrix method
  90. Theoretical Characterisation of the Electronic Excitation in Liquid Water
  91. Theoretical Study of the Thermodynamics of a Solvated Peptide: Contryphan Vn
  92. On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions
  93. Electronic properties of formaldehyde in water: a theoretical study
  94. Statistical Mechanics and Thermodynamics of Simulated Ionic Solutions