All Stories

  1. Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation
  2. Ion mobility–mass spectrometry of palytoxin-like compounds produced by Ostreopsis cf. ovata
  3. The multimerization pathway of the glucocorticoid receptor
  4. Oleuropein Aglycone, an Olive Polyphenol, Influences Alpha-Synuclein Aggregation and Exerts Neuroprotective Effects in Different Parkinson’s Disease Models
  5. Induction of the Inflammasome by the SARS‐CoV‐2 Accessory Protein ORF9b, Abrogated by Small‐Molecule ORF9b Homodimerization Inhibitors
  6. Shedding Light on Dark Chemical Matter: The Discovery of a SARS-CoV-2 Mpro Main Protease Inhibitor through Intensive Virtual Screening and In Vitro Evaluation
  7. The Discovery of inhibitors of the SARS-CoV-2 S protein through computational drug repurposing
  8. Assessment of the bound conformation of bombesin to the BB1 and BB2 receptors
  9. Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening
  10. A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics
  11. Autochthonous Peruvian Natural Plants as Potential SARS-CoV-2 Mpro Main Protease Inhibitors
  12. A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance
  13. α4-α5 Helices on Surface of KRAS Can Accommodate Small Compounds That Increase KRAS Signaling While Inducing CRC Cell Death
  14. Shedding light on the binding mechanism of kinase inhibitors BI-2536, Volasetib and Ro-3280 with their pharmacological target PLK1
  15. Effects of solvents on the conformational profile of Balaram's peptide: a computational study
  16. Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation
  17. Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 Mpro Protease through Virtual Screening
  18. Unravelling Constant pH Molecular Dynamics in Oligopeptides with Explicit Solvation Model
  19. Fragment dissolved molecular dynamics: a systematic and efficient method to locate binding sites
  20. On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides
  21. Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides
  22. Multigram scale synthesis of polycyclic lactones and evaluation of antitumor and other biological properties
  23. Toward understanding calmodulin plasticity by molecular dynamics
  24. Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
  25. The first theoretical structure for the K-Ras/Calmodulin complex
  26. Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
  27. Exploring potential energy surfaces with gentlest ascent dynamics in combination with the shrinking dimer method and Newtonian dynamics
  28. Substituted tetrahydroisoquinolines: synthesis, characterization, antitumor activity and other biological properties
  29. A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
  30. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations
  31. Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase
  32. Binding of the anticancer drug BI-2536 to human serum albumin. A spectroscopic and theoretical study
  33. Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory
  34. Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations
  35. One-pot synthesis of 4-aminated pyrrolo[2,3-d]pyrimidines from alkynylpyrimidines under metal-catalyst-free conditions
  36. Molecular Topology Applied to the Discovery of 1-Benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a Non-Ligand-Binding-Pocket Antiandrogen
  37. Molecular dynamics analysis of the interaction between the human BCL6 BTB domain and its SMRT, NcoR and BCOR corepressors: The quest for a consensus dynamic pharmacophore
  38. Design of an interface peptide as new inhibitor of human glucose-6-phosphate dehydrogenase
  39. Microwave-Assisted Synthesis of Substituted Pyrrolo[2,3-d]pyrimidines
  40. Atomic Level Rendering of DNA-Drug Encounter
  41. Structure-based approach to the design of BakBH3 mimetic peptides with increased helical propensity
  42. Structural analysis of the inhibition of APRIL by TACI and BCMA through molecular dynamics simulations
  43. A benchmark calculation for the fuzzy c-means clustering algorithm: initial memberships
  44. Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins
  45. Diphenyl Urea Derivatives as Inhibitors of Transketolase: A Structure-Based Virtual Screening
  46. Cyclin-dependent kinases 4 and 6 control tumor progression and direct glucose oxidation in the pentose cycle
  47. Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-xLProtein
  48. The Methylerythritol Phosphate (MEP) Pathway for Isoprenoid Biosynthesis as a Target for the Development of New Drugs Against Tuberculosis
  49. Predicting binding energies of CDK6 inhibitors in the hit-to-lead process
  50. Design of novel ligands of CDP-methylerythritol kinase by mimicking direct protein-protein and solvent-mediated interactions
  51. RED: A Set of Molecular Descriptors Based on Rényi Entropy
  52. Homology modeling of Mycobacterium tuberculosis 2C-methyl-d-erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis
  53. Corrigendum to “Homology modeling of human transketolase: Description of critical sites useful for drug design and study of the cofactor binding mode” [J. Mol. Graph. Model. 27 (2009) 723–734]
  54. Analysis of the basis set and correlation effects on the computation of molecular polarizabilities using molecular polarization maps
  55. Mimicking direct protein–protein and solvent-mediated interactions in the CDP-methylerythritol kinase homodimer: a pharmacophore-directed virtual screening approach
  56. Homology modeling of human Transketolase: Description of critical sites useful for drug design and study of the cofactor binding mode
  57. Conformationally Restricted Hydantoin-Based Peptidomimetics as Inhibitors of Caspase-3 with Basic Groups Allowed at the S3 Enzyme Subsite
  58. Protein-protein recognition as a first step towards the inhibition of XIAP and Survivin anti-apoptotic proteins
  59. Comparative Evaluation of MMPBSA and XSCORE To Compute Binding Free Energy in XIAP−Peptide Complexes
  60. Pseudometrics from three-positive semidefinite similarities
  61. Reducing CDK4/6-p16INK4a interface. Computational alanine scanning of a peptide bound to CDK6 protein
  62. Assessment of the performance of cluster analysis grouping using pharmacophores as molecular descriptors
  63. Synthesis and evaluation of diverse analogs of amygdalin as potential peptidomimetics of peptide T
  64. Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xLand Bcl-2 proteins
  65. Structural Analysis of the Inhibition of Cdk4 and Cdk6 by p16INK4athrough Molecular Dynamics Simulations
  66. The aluminium–acetylene interaction: structure, coordination modes, vibrational frequencies and hyperfine coupling constants. The density functional point of view
  67. Analysis of the convergence of the general coupling operator method for one-configuration-type wave functions
  68. Localized orbitals in nonmetallic ring systems
  69. Direct determination of localized Hartree–Fock orbitals as a step toward N scaling procedures
  70. On the bonding mechanism of CO to Pt(111) and its effect on the vibrational frequency of chemisorbed CO
  71. Ab initio cluster model study of geometry and bonding character of atomic nitrogen chemisorbed on the Cu(100) and Ag(100) surfaces
  72. Ab Initio Study of the Magnetic Coupling in Na6Fe2S6
  73. Density functional potential energy hypersurface of protonated ozone: A comparison between different gradient-corrected nonlocal functionals
  74. Using full-CI algorithms in Bethe-Goldstone-type expansions of the correlation energy
  75. Consequences of chemical bonding on the adiabaticity of gas-surface reactions
  76. The importance of correlation effects on the bonding of atomic oxygen on Pt(111)
  77. Adiabatic and diabatic representations of potential energy curves for the (NaRb)+ system
  78. Active sites of Pt surfaces from ab initio cluster model molecular electrostatic potential maps
  79. Ab initioelectronic structure of PtH+, PtH, Pt2, and Pt2H from a one‐electron pseudopotential approach
  80. Calculation of proton affinities and absolute gas basicities of X3 group VI triatomics: a density functional study
  81. Origin of magnetic coupling inLa2CuO4
  82. Origin of the Large N 1s Binding Energy in X-ray Photoelectron Spectra of Calcined Carbonaceous Materials
  83. An efficient improvement of the string-based direct selected CI algorithm
  84. Origin of the vibrational shift of CO chemisorbed on Pt(111)
  85. Performance of correlation functionals inab initiochemisorption cluster-model calculations: Alkali metals on Si(111)
  86. Nature of bonding of alkali metals to Si(111)
  87. Bonding geometry and mechanism of NO adsorbed on Cu2O(111): NO activation by Cu+ cations
  88. Energy partitioning using two-electron average matrices
  89. Bonding of atomic oxygen to Cu(100) and Ag(100) surfaces: a study of the nature of the interaction
  90. Cluster model description of the chemisorption bond: effect of the cluster model electronic state
  91. The analysis of the chemisorption bond from uncorrelated and correlated cluster model wave functions
  92. The full-CI energy of the NH3 molecule in a DZP basis set
  93. Electronic and geometrical structures of Pt3 and Pt4. An ab initio one-electron proposal
  94. Basis-Modified hydrogen atoms as embedding atoms inab initio chemisorption cluster model calculations on Si surfaces
  95. Bonding of atomic oxygen to Cu(100) and Ag(100) surfaces: a theoretical comparative study
  96. The ionicity of halogens chemisorbed on mercury revisited
  97. The orthogonal valence bond interpretation of ab initio chemisorption cluster model wavefunctions
  98. The cluster model configuration interaction approach to the study of chemisorption on metal and semiconductor surfaces
  99. The nature of the chemical bond in simple oxides: A theoretical journey from the ionic model to the ab initio configuration interaction approach
  100. Madelung fields from optimized point charges forab initiocluster model calculations on ionic systems
  101. Size-consistent selected configuration interaction calculations. A few tests of efficiency
  102. Ab initiovalence-bond cluster model for ionic solids: Alkaline-earth oxides
  103. Evidence for two different bonding mechanisms of Al on Si(111)
  104. A numerical test on the size consistency of some multireference configuration interaction approaches
  105. The nature of the bonding of atomic Al to Si(111): is there a specific site-bond relationship?
  106. Quasi-classical trajectory study of the dynamics of the reaction O(3P)+CS2(X1∑+g)→CS(X1∑+)+SO(X3∑−) using two model potential energy surfaces
  107. Reliability of atomic natural orbital basis sets in calculations involving pseudopotentials
  108. Treating large intermediate spaces in the CIPSI method through a direct selected CI algorithm
  109. An analysis of 3d correlation effects in the bonding of atomic oxygen to Cu(100)
  110. Selected versus complete configuration interaction expansions
  111. Effect of electron correlation on the electrostatic potential distribution of molecules
  112. Differential correlation effects in chemisorption cluster model calculations: an FCI study
  113. An ab initio study of the collinear reaction of Fe+ (4F) and Fe+ (6D) with H2
  114. On the potential energy surface for collinear OH+2 (4Σ−)
  115. The effect of dynamical correlation on the valence wavefunction of molecules: Dressed complete active space self-consistent field calculations
  116. On the performance of atomic natural orbital basis sets: A full configuration interaction study
  117. Chemisorption of group-III metals on the Si(111) and Ge(111) surfaces: Anab initiostudy
  118. Electronic structure of Rh, RhH, and Rh2 as derived from ab initio (configuration interaction) calculations
  119. Reliability of one‐electron approaches in chemisorption cluster model studies: Role of core‐polarization and core–valence correlation effects
  120. Ab initio study of the ground and low‐lying states of FeH
  121. Non-empirical cluster-model study of the relaxation of (111) surfaces of C, Si, Ge
  122. Taking into account non-dynamical correlation effects in ab initio chemisorption cluster model calculations
  123. Ab initio self‐consistent field and configuration interaction study of Cu5O and Ag5O as models for oxygen chemisorption on Cu(100) and Ag(100)
  124. Neutral versus ionic interactions in ab initio chemisorption cluster model calculations: halogens on mercury
  125. Ground and low‐lying states of FeH+ as derived from ab initio self‐consistent field and configuration interaction calculations
  126. Ab initio cluster model approach to the chemisorption on mercury
  127. Doublet instability and the molecular structure of AlO2
  128. Approximate natural orbitals and the convergence of a second order multireference many‐body perturbation theory (CIPSI) algorithm
  129. Chemisorption of atomic aluminum on Si(111): Evidence for an adsorbate-induced relaxation based onab initiocluster-model calculations
  130. Molecular structure and vibrational frequencies of AlxOy (x=1,2; y⩽3) derived from ab initio calculations
  131. On the inversion barriers of group 15 tricoordinate hydrides and halides: An ab initio study using analytical gradients
  132. Ab initio cluster model approach to the chemisorption of hydrogen on mercury
  133. The role of d electrons in ab initio chemisorption cluster model calculations. Atomic hydrogen on Cu(100) and Ag(100)
  134. Dynamical and nondynamical correlation effects inabinitiochemisorption cluster model calculations. Ground and low lying states of H on Cu(100) and Ag(100)
  135. Mixed pseudo-potential approach to the on-top chemisorption of atomic hydrogen on the (100) silver surface
  136. The molecular structure of bicyclo[1.1.0]tetraarsane from ab initio calculations using analytical gradients
  137. Theoretical evidence for two geometrical isomers of silver oxide (AgO2)
  138. Nonempirical cluster-model study of the chemisorption of atomic hydrogen on the (111) surface of diamondlike crystals
  139. Energy levels in the jj coupling scheme
  140. Convergence of a multireference second-order mbpt method (CIPSI) using a zero-order wavefunction derived from an MS SCF calculation
  141. Interpretation of the chemisorption bond based in the partitioning energy scheme in the RHF-MINDO/3 method: Adatoms on graphite
  142. The effect of electron correlation in the interaction of atomic hydrogen with Ben clusters 3≤n≤7
  143. Vibrational frequencies of halogens adsorbed on Ag (100) based on ab initio cluster model calculations
  144. Ab initio study of the superoxides of Group 13 metals
  145. Molecular structure, vibrational frequencies and ionization potential of tin dihalides
  146. An ab initio study of the interaction of atomic hydrogen with cluster models simulating the (100) and (110) silver surfaces
  147. A theoretical study of relaxation and reconstruction of the (111) surface of diamond
  148. On the use of frozen orbitals in molecular orbital cluster calculations: Cl on Si(111)
  149. Cu as a one-electron atom: Molecular structure and dissociation energy of CuOH
  150. Ab initiocluster-model study of the on-top chemisorption of F and Cl on Si(111) and Ge(111) surfaces
  151. MINDO/3 potential energy surface for hydrogen-graphite system: Active sites and migration
  152. Molecular structure of copper(I) hydroxide and copper hydroxide(1-) (Cu(OH)2-). An ab initio study
  153. Theoretical analysis of bonding in monomeric and polymeric C5H5M compounds
  154. Ab initio molecular structure of Xn,H2n, compounds, (X = Si, Ge, Sn; n = 3, 4)