The NNTMM code: Mathematical modeling, optimization, and data analysis through neural networks

The concept, functional capabilities, graphic interface, and application technology for the NNTMM code (Neural Network Tool for Mathematical Modeling), designed for analyzing large amounts of experimental and computational data in an interactive mode, are described. The software can be used to solve a wide range of applied problems where automated extraction of meaningful information from randomly presented data is required, along with data classification, clear representation of established relationships and dependences, analysis of parameter importance, and prediction. Examples of using the NNTMM code to analyze data in controlled nuclear fusion problems are presented.     

Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

The highly pathogenic avian influenza virus (HPAIV) A subtype H5N1 is causing threat to human health over the years. Phylogenetic analysis is an important tool for analyzing the evolution of influenza. A novel phylogenetic algorithm based on a new protein distance measure derived from the informational spectrum method (ISM) has been presented. The new phylogenetic approach allows assessment of functional evolution of protein sequences. The new ISM-based phylogenetic approach has been found to overcome some drawbacks of other phylogenetic approaches, particularly concerning sensitivity to a single mutation, deletion and the position of the mutation. The ISM-based approach applied to hemagglutinin subunit 1 protein (HA1) of HPAIV A subtype H5N1 viruses in Egypt between 2006 and 2011, revealed clear clustering in two groups, with one growing group of H5N1 viruses after 2009 with increased number of human infections with H5N1. Four group-specific mutations are identified which are important for increased human tropism and the pandemic potential.     

Reverse fragment based drug discovery approach via simple estimation of fragment contributions

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Diastereospecific ring cleavage of bornane-2,3-dione in the Bucherer-Bergs reaction

A novel regio- and diastereospecific ring cleavage of bornane-2,3-dione (camphor quinone) under Bucherer-Bergs reaction conditions has been investigated. The simplicity of this transformation provides a novel and straightforward synthetic pathway to enantiopure derivatives of cyclopentane carboxylic acid as well as functionalized hydantoins in just two steps, starting from inexpensive and easily available camphor.     

Rearrangement of O,O’-bis(2-benzylideneaminophenyl) phenylphosphonite into 1,6,7-triphenyl-3,4:9,10-dibenzo-2,11-dioxa-5,8-diaza-1-phosphatricyclo[6.3.0.01,5]undeca-3,9-diene

Keeping of O,O’-bis(2-benzylideneaminophenyl) phenylphosphonite in a CCl4 solution for 50 days resulted in its spontaneous rearrangement into 1,6,7-triphenyl-3,4:9,10-dibenzo-2,11-dioxa-5,8-diaza-1-phosphatricyclo[6.3.0.01,5]undeca-3,9-diene, a representative of spirophosphoranes with P–N bonds.     

Efficient Resolution of Some Monoprotected Derivatives of Corey Lactone

Racemic monoprotected at primary hydroxy group Corey lactones were resolved using (1S,2R,5R)-6,6-dimethyl-4-oxo-3-oxabicyclo-[3.1.0]hexan-2-ol as a chiral auxiliary reagent of hemiacylal chemotype.