Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.3K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
15.3K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
5.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same author

BindPred: a framework for predicting protein-protein binding affinity from language model embeddings.

Bioinformatics (Oxford, England)·2026
Same author

MechFind: a computational framework for de novo prediction of enzyme mechanisms.

Nature communications·2026
Same author

High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis.

Nature communications·2026
Same author

Building an expanded bio-based economy through synthetic biology.

Biotechnology advances·2025
Same author

Metabolic flux and resource balance in the oleaginous yeast Rhodotorula toruloides.

Metabolic engineering·2025

Related Experiment Video

Updated: Apr 20, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

1.4K

The Iterative Protein Redesign and Optimization (IPRO) suite of programs.

Robert J Pantazes1, Matthew J Grisewood, Tong Li

  • 1Chemical Engineering Department, University of California, Santa Barbara, 3357 Engineering II, Santa Barbara, California, 93106.

Journal of Computational Chemistry
|December 3, 2014
PubMed
Summary

This study introduces the Iterative Protein Redesign and Optimization (IPRO) software suite, which uses algorithms to computationally redesign protein sequences for improved function in biotechnology and medicine.

Keywords:
IPROantibodiescomputational designenzymesproteins

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K

Related Experiment Videos

Last Updated: Apr 20, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

1.4K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K

Area of Science:

  • Biomolecular engineering
  • Computational biology
  • Protein design

Background:

  • Proteins are crucial biomolecules with broad applications in biotechnology and medicine.
  • Native proteins often require redesign to enhance performance metrics like binding affinity, specificity, and enzymatic activity.
  • Computational methods can optimize protein library design by focusing on sequences that improve computationally accessible proxies.

Purpose of the Study:

  • To provide an overview of the Iterative Protein Redesign and Optimization (IPRO) software suite.
  • To detail the methods, terminology, algorithms, and implementation of IPRO.
  • To highlight applications of IPRO in protein engineering.

Main Methods:

  • The Iterative Protein Redesign and Optimization (IPRO) suite of programs integrates computational tools.
  • IPRO enables alteration of protein binding affinity and specificity.
  • IPRO facilitates binding pocket grafting, antibody structure prediction, enzymatic activity enhancement, and mutant binding energetics assessment.

Main Results:

  • The manuscript details the methods, input language, algorithmic specifics, and implementation of the IPRO software.
  • IPRO offers a comprehensive environment for various protein redesign tasks.
  • Application highlights demonstrate the utility of IPRO in protein engineering.

Conclusions:

  • The IPRO suite provides an integrated computational environment for protein redesign.
  • IPRO supports diverse applications including affinity tuning, scaffold design, antibody prediction, and enzyme optimization.
  • The IPRO software is available for download, facilitating advancements in protein engineering.