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Title: Year 2 Report: Protein Function Prediction Platform

Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort requiredmore » to select and characterize protein biomarkers.« less
Authors:
Publication Date:
OSTI Identifier:
1043635
Report Number(s):
LLNL-TR-554191
TRN: US201214%%149
DOE Contract Number:
W-7405-ENG-48
Resource Type:
Technical Report
Research Org:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICAL METHODS AND COMPUTING; BIOLOGICAL PATHWAYS; BIOLOGY; DESIGN; FORECASTING; FUNCTIONALS; MODIFICATIONS; PATHOGENS; PROCESSING; PROTEIN STRUCTURE; PROTEINS; SIMULATION