Related Experiment Video
Updated: Aug 18, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure
Milana Frenkel-Morgenstern1, Hillary Voet, Shmuel Pietrokovski
1Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100, Israel.
Motivation:
Improved comparisons of multiple sequence alignments (profiles) with other profiles can identify subtle relationships between protein families and motifs significantly beyond the resolution of sequence-based comparisons.
Results:
The local alignment of multiple alignments (LAMA) method was modified to estimate alignment score significance by applying a new measure based on Fisher's combining method. To verify the new procedure, we used known protein structures, sequence annotations and cyclical relations consistency analysis (CYRCA) sets of consistently aligned blocks. Using the new significance measure improved the sensitivity of LAMA without altering its selectivity. The program performed better than other profile-to-profile methods (COMPASS and Prof_sim) and a sequence-to-profile method (PSI-BLAST). The testing was large scale and used several parameters, including pseudo-counts profile calculations and local ungapped blocks or more extended gapped profiles. This comparison provides guidelines to the relative advantages of each method for different cases. We demonstrate and discuss the unique advantages of using block multiple alignments of protein motifs.
More Related Videos
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
07:49Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Related Concept Videos
Protein Organization
The primary structure of a protein is its amino acid sequence.
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces
Ligand Binding and Linkage