FoldMiner and LOCK 2

FoldMiner and LOCK 2 provide protein structure alignment and unsupervised motif discovery to identify structural neighbors and characteristic motifs for inferring protein function and evolutionary relationships.

Key Features:

• Integrated structure alignment and motif discovery: Combines structure alignment with motif discovery and iteratively refines results to improve motif definition and detection sensitivity.
• Unsupervised motif discovery: Discovers structural motifs without prior annotation to characterize recurring structural patterns among aligned proteins.
• Structural similarity searches: Performs structural similarity searches to identify proteins with shared folds or local structural neighborhoods.
• Automated alignment against single-domain databases: Executes automated runs that align a query structure against databases of single-domain protein targets.
• Manual refinement option: Provides an option for manual refinement of results following automated analyses.
• LOCK 2 algorithm integration: Integrates the LOCK 2 algorithm for rapid alignment of query structures against specified, smaller sets of target proteins.

Scientific Applications:

• Structure–function inference: Identifies structural motifs and neighbors to infer relationships between protein structure and function.
• Functional annotation and prediction: Supports prediction of protein function by detecting characteristic structural motifs shared with annotated proteins.
• Evolutionary relationship analysis: Enables exploration of evolutionary relationships through detection of conserved structural motifs and fold similarities.
• Exploratory to detailed structural analyses: Facilitates both broad exploratory searches for structural neighbors and focused, detailed analyses of motif-containing regions.

Methodology:

Performs structure alignment and structural similarity searches combined with unsupervised motif discovery, iteratively refining motifs and alignments; supports automated alignment of queries against databases of single-domain targets and rapid alignment against specified target sets via the LOCK 2 algorithm.