MOTIVATION Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular com...

Binding of the Tetrahymena ribozyme's oligonucleotide substrate (S) involves P1 duplex formation with the ribozyme's internal guide sequence (IGS) to give an open complex, followed by docking of the P1 duplex into the catalytic core via tertiary interactions to give a closed complex. The overall binding energies provided by 2' OH groups on S and IGS have been measured previously. To obtain the ...

lanthanide(iii) chloro complexes of 4[n-(4’-hydroxy-3’-methoxybenzalidene) amino] antipyrine semicarbazone (hmbaaps) (i) and 4[n-(3’,4’,5’-trimethoxybenzalidene) amino] antipyrine semicarbazone (tmbaaps) (ii) with the general composition lncl3.2l (ln = la, pr, nd, sm, gd, tb, dy or ho; l = hmbaaps or tmbaaps) are reported. all the complexes were synthesized in ethanolic medium and refluxed the ...

Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activate...

Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally determined values. In parsing our results based on specific functional groups of do...

RNA-binding proteins play many essential roles in the regulation of gene expression in the cell. Despite the significant increase in the number of structures for RNA-protein complexes in the last few years, the molecular basis of specificity remains unclear even for the best-studied protein families. We have developed a distance and orientation-dependent hydrogen-bonding potential based on the ...

The interplay between two important non-covalent interactions involving aromatic rings (namely anion-pi and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion-pi and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen-bond donor/acceptor molecule is as long as ...

The combination of physicochemical properties and energetic parameters derived from protein-ligand complexes play a vital role in determining the biological activity of a molecule. In the present work, protein-ligand interaction energy along with logP values was used to predict the experimental log (IC50) values of 25 different kinase-inhibitors using multiple regressions which gave a correlati...

The electronic structure of the N-heterocyclic carbene (NHC) functionalized polyoxometalate [K(PW(9)O(34))(2)(cis-WO(2))(cis-RuLMe(2))](12-) (1) is studied computationally; and its Ru-NHC bonding situation is compared with other monometallic Ru-NHC complexes, as well as other representative carbene complexes. The DFT analysis further supports the low spin configuration, S = ½, as the ground sta...