Simulations of Protein Motions

• Relationships between Structure, Sequence and Function
• Interaction Models for Proteins and Nucleic Acids
• Computational Tools to Aid Developing Molecular Models and Design of New Molecules and Drugs

Systems Biology and the integration of large-scale biological data

• Discovering Missing Connections in the Protein-protein Network
• Deriving Functional Clusters of Interacting Proteins
• Probing the Interactome to Identify Essential Proteins

Elastic models of protein motions

• Coarse-grained for Extremely Large Systems - ribosome, spliceosome, viruses
• Protein Contact Predictions

• Computer Generated Protein Library
• Protein Transitions - e.g. Domain Swapping
• Mixed Coarse-grained - from Atomic to Multi-residue
• Normal Modes of Motion
• Biological Mechanisms
• Application to Molecular Modeling

Structure predictions

• Secondary Structures
• Protein Contact Predictions
• Computer Generated Protein Library
• Post-translational Modification Sites

Datamining from structures

• Interactions within Proteins
• Interactions between Proteins
• Interactions between Proteins and Nucleic Acids
• Structure Fragment Libraries
• Residue Orientations in Proteins

Genomic data

• Microarray Analyses
• Comparisons between Genomes
• Network Structure and Topologies
• Improving Gene Annotations

High Performance Computing and Algorithms

• Efficient Generation of Conformations
• Evaluation of Computer Architectures for Bioinformatics Applications