NCBI Intramural Research Projects, 1994-1995

Structure/Function

• The HMG-1 box protein family and homology model building of the HMG-1 box structural domain
• Sequence analysis of the histone proteins and the histone fold motif
• Steroid responsiveness and steroid receptor binding sites in the HIV-1 LTR
• Proteins that interact with ras-like GTPases
• Information and molecular recognition in DNA-protein interactions
• Identification and mapping of the human homolog of the yeast cell cycle gene
• Subtle sequence patterns in DNA-binding complexes
• Computer analysis of low-complexity amino acid sequences
• Molecular novelty and conservation in bacterial protein sequences
• Identification of fossil sequences by exhaustive comparison of protein sequences from evolutionarily distant organisms
• Analysis of conserved amino acid sequence motifs in NTPases
• Cold shock domain (CSD) protein motif
• DNA sequence complexity and mutational dynamics

Biomolecular Structure

• Analysis of packing contacts in protein crystals
• Extended two-dimensional lattice models of proteins
• 3-D computer modeling of ribonucleic acids
• Structure prediction by protein threading
• Energy distribution of the compact states of a peptide

Genome Analysis

• Inherited disease genes identified by positional cloning
• Multiple alignment of the complete genome of HTLV-I and STLV-I
• Informatics analysis of the E. Coli genome
• Genome organization and evolution of RNA viruses
• Sequence analysis methods adapted to large scale sequencing projects
• Comprehensive computer analysis of E. coli genes
• Identification of the Kallmann syndrome gene (xp22.3) and of new genes in the HLA class III region (6p21.3)

Theory of Sequence Analysis

• Statistics of sequence comparison
• A depth-first search algorithm for detecting patterns in protein sequences
• Gibbs sampling methods for the analysis of biopolymer sequence data
• Analysis of reliability of molecular sequence data

Hardware Design

• Bioscan--a VLSI-based system for biosequence analysis

Software and Database Design

• Unification of biotechnology information
• Portable toolbox for scientific software
• Design and uses of a public resource of expressed sequence tags
• Development of a transcription factors database
• Databases for molecular modeling
• A representative set of protein sequences for similarity searching

Text Retrieval and Document Analysis

• Textual information retrieval
• Automatic Bayesian methods in text retrieval
• A document processing system
• Strategies for finding relevant documents among neighbor lists
• Situtation theory as a model for ontological engineering and knowledge
• Gibbs sampling as an approach to document retrieval