In this paper we present a novel method to describe the pose (position and orientation) distribution of amino acid residue pairs within a protein, which are proximal in space and distal in sequence.While the Ramachandran plot provides information of protein conformations using the φ and ψ angles between sequentially proximal residues, our method can offer six-dimensional relative pose informati...

Many studies have used position-specific scoring matrices (PSSM) profiles to characterize residues in protein structures and to predict a broad range of protein features. Moreover, PSSM profiles of Protein Data Bank (PDB) entries have been recalculated in many works for different purposes. Although the computational cost of calculating a single PSSM profile is affordable, many statistical studi...

A great deal of system and human effort is expended to collect detailed technical measurements. These measurements are usually stored in some form of a Performance Database, or PDB. However, these data do little to help us understand the purpose of those systems: supporting our business. These basic performance measures tell us very little about the systems’ business value. To understand that b...

UNLABELLED To aid detailed comparison of a large number of macromolecular structures, Resmap imports Protein Data Bank files and represents subunit/domain interfaces as two-dimensional networks. AVAILABILITY http://www.kumc.edu/biochemistry/resmap/. SUPPLEMENTARY INFORMATION Default definitions and directions for graphically managing networks are available at the same website.

The performance database (PDB) stores performance-related data gathered during workflow enactment. We argue that, by carefully understanding and manipulating these data, we can improve efficiency when enacting workflows. This paper describes the rationale behind the PDB, and proposes a systematic way to implement it. The prototype is built as part of the Advanced Data Mining and Integration Res...

An iterative process for improving the completeness and quality of atomic models automatically built at moderate resolution (up to about 2.8 A) is described. The process consists of cycles of model building interspersed with cycles of refinement and combining phase information from the model with experimental phase information (if any) using statistical density modification. The process can lea...

We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over 1,000 structures from the Protein Data Bank (PDB). Each CASP2 target sequence was scored against this library of HMMs. In addition, an HMM was built for each of the target sequences and all of the sequences ...

Despite their general success in the heuristic search community, pattern database (PDB) heuristics have, until very recently, not been used by the most successful classical planning systems. We describe a new efficient implementation of pattern database heuristics within the Fast Downward planner. A planning system using this implementation is competitive with the state of the art in optimal pl...

It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlightin...