Exploiting whole-PDB analysis in novel bioinformatics applications

Thesis

The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explore...

Expand abstract

Authors: Ramraj, V

• Publication date: 2014
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: peptides; disorder prediction; parallelization; PDB; nearest-cell; proteins; space group; neural network; crystallography; protein data bank; clustering; nearest cell; unit cell; bioinformatics; fragments; RONN; training; structural biology; MoreRONN; OpenMP
• Subjects: Membrane proteins; Mathematical genetics and bioinformatics (statistics); Enzymes; Bioinformatics (biochemistry); Chemistry & allied sciences; Applications and algorithms; Bioinformatics (technology); Program development and tools; Polymers Amino acid and peptide chemistry; Mass spectrometry; Computational biochemistry; Genetics (life sciences); Biomedical engineering; Structural genomics; Computationally-intensive statistics; Computing; Bioinformatics (life sciences); Computer science (mathematics); Theory and automated verification; Protein chemistry; Biology (medical sciences); Medical sciences; Crystallography; Scalable systems; Medical Sciences; Life Sciences; NMR spectroscopy; Software engineering; Genetics (medical sciences); Protein folding; Physical Sciences