RRDistMaps

RRDistMaps computes and visualizes generalized protein distance maps within UCSF Chimera to identify and compare intramolecular contacts and conformational changes.

Key Features:

• Generalized Distance Maps: Represents contacts as continuous distance ranges instead of binary (yes/no) contact maps to capture graded interaction patterns.
• Visualization of Conformational Changes: Enables examination of local changes at binding sites and global alterations such as hinge motions by comparing distance patterns between unbound and bound states.
• Residue-Pair Selection and Mapping: Allows selection and detailed examination of specific residue pairs and maps distance information to structures in Chimera.
• Long-Range Motion Identification: Detects long-range residue motions to reveal dynamic behaviors and intramolecular coupling.
• Sequence Alignment Integration: Aligns sequences to facilitate simultaneous comparison of distance maps across different proteins or states.

Scientific Applications:

• Ligand Binding Analysis: Comparing distance maps between unbound and bound states to identify conformational changes associated with ligand binding.
• Allosteric Regulation Studies: Identifying distance changes and long-range couplings that underlie allosteric regulation.
• Protein Folding/Unfolding Investigations: Monitoring pairwise distance variations relevant to folding and unfolding transitions.
• Intramolecular Contact Network Mapping: Elucidating contact patterns and dynamic interaction networks within proteins.

Methodology:

RRDistMaps computes generalized contact maps by analyzing pairwise variations in intramolecular contacts across different protein states and is implemented as part of UCSF Chimera.