Related Experiment Video
Updated: Jul 17, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
Walking through the protein sequence space: towards new generation of the homology modeling
Zakharia M Frenkel1, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zakharf@research.haifa.ac.il
Abstract:
A new method is proposed to reveal apparent evolutionary relationships between protein fragments with similar 3D structures by finding "intermediate" sequences in the proteomic database. Instead of looking for homologies and intermediates for a whole protein domain, we build a chain of intermediate short sequences, which allows one to link similar structural modules of proteins belonging to the same or different families. Several such chains of intermediates can be combined into an evolutionary tree of structural protein modules. All calculations were made for protein fragments of 20 aa residues. Three evolutionary trees for different module structures are described. The aim of the paper is to introduce the new method and to demonstrate its potential for protein structural predictions. The approach also opens new perspectives for protein evolution studies.
Related Concept Videos
Protein Families
Molecular Models
Protein and Protein Structure
A protein's shape is critical to its function. For example, an enzyme can...
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 and Protein Structures
A protein's shape is critical to its function. For example, an enzyme can...
Conservation of Protein Domains
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

