Conformations and electronic properties of a series of imidazobenzodiazepines are investigated by AM1 semi-empirical quantum mechanics method. It is shown that substitution of Cl in position 7 instead of 8, changes the geometry of the seven membered lactam ring; this may put the N5 nitrogen in a better positon to act as a hydrogen bond acceptor, and the phenyl ring in position 6 is probably...

The results of MNDO, AM1 and PM3 semi-empirical calculations and HF/6-31G*, MP/6-31G*, MP2/6-311+G**, and B3LYP/6-311G** and QCISD/6-31G* ab initio methods for angle strain and conjugation effects in twist-boat, boat, and half-chair geometries of (Z,Z,Z)-cycloocta-1,3,5-triene indicate that all methods, except PM3, predict wrong ordering of the conformations.

We examine the conformations of a model for underand overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spat...

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed...

BACKGROUND Extraction and investigation of TAXOL from Pestalotiopsis breviseta (Sacc.) using protein docking, which is a computational technique that samples conformations of small molecules in protein-binding sites. Scoring functions are used to assess which of these conformations best complements the protein binding site and active site prediction. MATERIALS AND METHODS Coelomycetous fungi ...

The complexity of molecular kinetics can be reduced significantly by a restriction to metastable conformations which are almost invariant sets of molecular dynamical systems. With the Robust Perron Cluster Analysis PCCA+, developed by Weber and Deuflhard [6], we have a tool available which can be used to identify these conformations from a transition probability matrix. This method can also be ...

Bispuupehenone, C(42)H(54)O(6), formally results from dimerization of puupehenone, which is constructed of sesquiterpene and benzene units. Bispuupehenone was isolated from the South China Sea sponge Dysidea sp. and the single-crystal X-ray diffraction analysis confirmed the previously reported structure. The mol-ecule is located on a twofold axis and the dimerization forms two fused dibenzopyr...

In recent years an effort has been made to supplement traditional methods for drug discovery by computer-assisted “structure-based design.” The structure-based approach involves (among other issues) reasoning about the geometry of drug molecules (or ligands) and about the different spatial conformations that these molecules can attain. This is a preliminary report on a set of tools that we are ...

In conformational analysis, the systematic search method completely maps the space but suffers from the combinatorial explosion problem because the number of conformations increases exponentially with the number of free rotation angles. This study introduces a new methodology of conformational analysis that controls the combinatorial explosion. It is based on a dimensional reduction of the syst...

We present an efficient and accurate clustering method for the analysis of protein-ligand docking datasets on large distributed-memory systems. For each ligand conformation in the dataset, our clustering algorithm first extracts relevant geometrical properties and transforms the properties into a single metadata point in the N-dimensional (N-D) space. Then, it performs an N-D clustering on the ...