Brief descriptions of research projects from 2005 and earlier.

• Novel Clustering Algorithms and Impact of Noise in Microarray Experiments (Herman & Yu, NLM)
• Folding simulations of cysteine-rich proteins (Sardiu, Doerr & Yu, NLM)
• Mutation rates in pseudogenes (Doerr & Yu, NLM)
• Mass spectrometry (Alves & Yu, NLM)
• Quantum chemical calculations on peptide systems with solvent (Janaki Mahadevan, NLM)
• Proton transfer process in bacteriorhodopsin (Yong Sok Lee, CIT)
• Understanding the physical mechanisms involved in the function of biological macromolecules (Sergio A. Hassan, CIT)
• Modeling of TRHR receptors (Xiang Zheng, NIDDK)
• Development of computer-intensive statistical procedures (James Troendle, NICHD)
• Conformation and design of tumor suppressor p53 (Yongping Pan, NCI)
• Towards Novel Therapeutics against HIV Infection and Drug Resistance (Ye Che, NHLBI)
• Statistical studies of microarrays (Lori Dodd, NCI)
• Interaction of Trehalose with lipid monolayers and bilayers (Anna Skibinsky, FDA)
• Molecular Simulation of Lipids (Jeff Klauda, NHLBI)
• Conformational Study of Small Molecules in Crystallographically Determined Structures (Rajeshri Karki, NCI)
• SNP detection within genomes (Jim Mullikin, NHGRI)
• Energy landscape of amyloidogenic peptide oligomerization (Gavin Tsai, NCI)
• Gas-phase peptide fragmentation (Chris Kinsinger, NIST)
• Self-assembly properties of beta-helical protein segments (Nurit Haspel, NCI)
• Molecular Dynamics Simulation of Protein Folding (Xiongwu Wu, NHLBI)
• Global optimization of peptide structure (Peter Steinbach, CIT)
• Gene mapping for hereditary deafness (Edward Wilcox, NIDCD)
• Genetic algorithms for protein folding (Douglas Vail, NHLBI)
• PET and EPR imaging (Calvin Johnson, CIT)
• NMR spectral lineshape analysis (Edward Sternin, NIAAA)
• Mapping protein surfaces (Gerhard Hummer, NIDDK)
• Gene expression analysis using cDNA microarrays (Seungchan Kim, CIT)
• Micelle characterization (Steven Bogusz, CBER)
• Lipid Bilayer structure and dynamics (Rick Venable, CBER)
• Estimation of Linkage from TDT data (J.D. Malley, CIT)
• Molecular modeling of HIV-1 integrase and complexes (Yun Tang, NCI)
• Statistical properties of microarray data (James Troendle, NICHD)
• Statistical approaches to identifying disease-related genes (David Pee, NCI)
• Raytraced images of complex macromolecules (Fred Dyda, NIDDK)
• Modeling of enzyme mechanism (Yong Sok Lee, NHLBI)
• A Transcriptome Map of Human Lung Cancer (Takeshi Fujii, NCI)
• Detection of similarity between distantly related proteins (Andrey Kajava, CIT)
• Dynamics/folding of peptides (In-Chul Yeh, NIDDK)
• Searching for new genes (James Vincent, NCI)
• Analysis of Loss of Heterozygosity data (Sally Hunsberger, NCI)
• Study of amyloid fiber organization (David Zanuy, NCI)
• Theoretical studies of enzyme catalysis (Morris Kraus, NIST)
• Protein folding & EM studies (Xiongwu Wu, NHLBI)
• Developing computational methods for studying transition processes in biological systems (Jhih-Wei Chu, MIT/NHLBI)
• Hybrid Monte-Carlo/MD replica exchange simulations (Roman Osman, MSSM)
• Molecular mechanisms of TRH receptor activation (Wei Huang, NIDDK)
• Replica Exchange Molecular Dynamics (Gavin Tsai, NCI)
• Enzyme Functions and Mechanisms (K. Gunasekaran, NCI)

---

Micelle characterization (Steven Bogusz, CBER) Kinetic models for biological motors (Yi-Der Chen, NIDDK) Simulations of solid state NMR (Rob Tycko, NIDDK) Microarray analysis software (Peter Munson, CIT) Microtubule conformational flexibility (Stewart Durell, NCI) Lipid Bilayer structure and dynamics (Rick Venable, CBER) Molecular modeling of HIV-1 integrase and complexes (Yun Tang, NCI) Kinetics of tubulin polymerization (Damien Hall, NIDDK) Identification of DNA sequences (Philip Krause, CBER) Particle Diffusion Simulations (Leonardo Dagdug, CIT) Protein denaturation by co-solutes (Daniel Harries, NICHD)