Multivariate analysis of properties of amino acid residues in proteins from a viewpoint of functional site prediction

Exploring chemistry with the fragment molecular orbital method

“…154 An interesting alternative to estimating the BSSE correction was proposed by Merz and coworkers, based on a parametrized statistical model. 155 For excited states, an excitation PIE is defined in eqn (7); these values provide useful information about the nonelectrostatic quantum effects of the environment upon the excitation energy of the chromophore, whereas the electrostatic contribution can be evaluated by comparing o M with the excitation energy of the standalone chromophore M. 114,115 Other types of analyses are represented by the visualized cluster analysis of protein-ligand interaction (VISCANA) 156 employing pair interactions in the clustering technique for the purpose of virtual ligand screening, two-dimensional maps of the interactions 157 and the multivariate analysis 158 developed for the functional site prediction.…”

Quantifying Inter-Residue Contacts through Interaction Energies

“…These graphs translate a protein structure into a set of nodes (defined as a single amino acid residue) interconnected by edges (defined as an electronic or steric interaction between two amino acid residues) . Edges are generally established by properties such as interatomic distances, hydrogen bonding, and interaction strength computed at the MM-level of theory. , Analyzing the topologies of RINs has already provided insight into structure–function features including protein stability, , allosteric regulation, , protein folding and dynamics, , and active site identification. − Building up from RINs, edges may also include metadata such as structural, chemical, or evolutionary properties . This forms a structural interaction fingerprint (SIFt or SIF) for each edge, and the analysis of SIFts has proven valuable in the domains of drug design and virtual screening. − …”

Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians

“…In the past decade, performing large-scale static and dynamic calculations has become essential in different areas of chemical research, including, e.g. , modeling the explicit solvation of chromophores, − the active sites of enzymes, , homogeneous clusters, − proteins, − photochemistry, , and the properties of crystals, , polymers, − and nanomaterials. , Performing ab initio electronic structure calculation on large systems has become significantly more practical, thanks to advances in computational hardware and new efficient algorithms. Density functional theory (DFT) calculations are now regularly performed for systems of up to O (10 3 ) atoms (using local functionals), although more stringent limitations are associated with post-Hartree–Fock (post-HF) methods that take increasing account of electron correlation.…”