New assessment of a structural alphabet

A DNA structural alphabet provides new insight into DNA flexibility

DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) class...

Detecting Protein Candidate Fragments Using a Structural Alphabet Profile Comparison Approach

Predicting accurate fragments from sequence has recently become a critical step for protein structure modeling, as protein fragment assembly techniques are presently among the most efficient approaches for de novo prediction. A key step in these approaches is, given the sequence of a protein to model, the identification of relevant fragments - candidate fragments - from a collection of the avai...

Structural Reliability: An Assessment Using a New and Efficient Two-Phase Method Based on Artificial Neural Network and a Harmony Search Algorithm

In this research, a two-phase algorithm based on the artificial neural network (ANN) and a harmony search (HS) algorithm has been developed with the aim of assessing the reliability of structures with implicit limit state functions. The proposed method involves the generation of datasets to be used specifically for training by Finite Element analysis, to establish an ANN model using a proven AN...

A Class of Two Generated Automaton Groups on a Three Letter Alphabet

Protein structure database search and evolutionary classification

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the sta...