Advances in computational protein design
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Updated: Mar 2, 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
Sheldon Park1, Xi Yang, Jeffery G Saven
1Makineni Theoretical Laboratories and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
Abstract:
Computational protein design continues to experience a variety of methodological advances. Several improvements have been suggested for the objective functions used to quantify sequence/structure compatibility. Disparate design strategies based upon dead-end elimination, simulated annealing and statistical design have each recently yielded striking successes involving de novo designed proteins with sizes on the order of 100 residues or greater. Such methods may be used to design new proteins, as well as to redesign natural proteins to facilitate structural and biophysical studies.
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