# Multi-objective optimization for designing structurally similar proteins with dissimilar sequences

https://mdr.nims.go.jp/datasets/142326e0-2353-4dd7-ad11-858786f16af5

## File

- [Multi-objective optimization for designing structurally similar proteins with dissimilar sequences.pdf](https://mdr.nims.go.jp/filesets/327dc411-671a-420a-8c34-001763466ce0/download) ([Detail](https://mdr.nims.go.jp/filesets/327dc411-671a-420a-8c34-001763466ce0.md))
- [TSTM-2025-0050_data.zip](https://mdr.nims.go.jp/filesets/429dfe49-5a2d-4ffa-96e2-ba7b80c356db/download) ([Detail](https://mdr.nims.go.jp/filesets/429dfe49-5a2d-4ffa-96e2-ba7b80c356db.md))

## Id

142326e0-2353-4dd7-ad11-858786f16af5

## Local identifier



## Visibility

open_to_public

## State

published

## Created at

2026-01-16T05:50:53.762526Z

## Updated at

2026-02-03T06:05:41.221666Z

## Published at

2026-01-19T03:21:35.375320Z

## Doi

https://doi.org/10.48505/nims.6136

## First published url

https://doi.org/10.1080/27660400.2025.2611575

## Date published

2026-12-31

## Recorded date published

2026-12-31

## Resource type

journal_article

## Manuscript type

accepted_manuscript

## Collection



## Title

- title: Multi-objective optimization for designing structurally similar proteins
    with dissimilar sequences
  title_type: original
  lang: en

## Description

- description: Recent advances in artificial intelligence technologies have accelerated
    the development of computational protein design techniques. Although the structure
    of the designed proteins has been the primary focus, diversity of designed amino
    acid sequences is another important aspect of protein design. To address the trade-off
    between reducing sequence similarity and improving structural similarity, simultaneous
    optimization of these two objectives can be effective. We present a method that
    integrates ProteinMPNN with the multi-objective optimization algorithm NSGA-II
    to design proteins that retain high structural similarity to a target while exhibiting
    low sequence similarity. Using Top7 as a reference protein, we demonstrate that
    our approach can design proteins with lower sequence similarity to the reference
    compared to the original ProteinMPNN, while maintaining comparable structural
    similarity.
  description_type: abstract
  lang: en

## Creator

- name: Ryo Akiba
  role: author
  organization: Institute of Science Tokyo
  department: a School of Life Science and Technology
- name: Yoshitaka Moriwaki
  role: author
- name: Ryuichiro Ishitani
  role: author
- name: Naruki Yoshikawa
  role: author

## Contact agent



## Publisher

organization: Taylor & Francis

## Managing organization



## Keyword

- subject: Protein design
  schema: not_defined
- subject: multi-objective optimization
  schema: not_defined
- subject: generative AI
  schema: not_defined

## Rights

- identifier: https://creativecommons.org/licenses/by/4.0/

## Other identifier(s)



## Data origin

- data_origin_type: other

## Embargo



## Journal

- title: Science and Technology of Advanced Materials
  issn: '27660400'
  volume: '6'
  article_number: " 2611575"

## Conference



## Related item



## Funding



## Instrument



## Instrument operator



## Instrument managing organization



## Measurement method



## Specimen



## Chemical composition



## Structure for specimen



## Structural feature for specimen



## Specific property for specimen



## Process for specimen treatment



## Computational method



## Energy level/transition state



## Software



## Custom property



## Fileset

- id: 327dc411-671a-420a-8c34-001763466ce0
  filename: Multi-objective optimization for designing structurally similar proteins
    with dissimilar sequences.pdf
  content_type: application/pdf
  size: 1284271
  md5: aa78088ca8148c0d51a7f4666f77471f
- id: 429dfe49-5a2d-4ffa-96e2-ba7b80c356db
  filename: TSTM-2025-0050_data.zip
  content_type: application/zip
  size: 8198548
  md5: 1386cdc68b43ccafff3dd62950208745

## Thumbnail

fileset_id: 327dc411-671a-420a-8c34-001763466ce0
filename: Multi-objective optimization for designing structurally similar proteins
  with dissimilar sequences.pdf