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Showing 1–10 of 10 results

Advanced filters: Author: Milot Mirdita Clear advanced filters

ColabFold: making protein folding accessible to all

ColabFold is a free and accessible platform for protein folding that provides accelerated prediction of protein structures and complexes using AlphaFold2 or RoseTTAFold.

Milot Mirdita
Konstantin Schütze
Martin Steinegger
ResearchOpen Access30 May 2022
Nature Methods

Volume: 19, P: 679-682
De novo discovery of conserved gene clusters in microbial genomes with Spacedust

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

Ruoshi Zhang
Milot Mirdita
Johannes Söding
ResearchOpen Access15 Sept 2025
Nature Methods

Volume: 22, P: 2065-2073
GPU-accelerated homology search with MMseqs2

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure prediction, and structural searches with Foldseek.

Felix Kallenborn
Alejandro Chacon
Martin Steinegger
ResearchOpen Access18 Sept 2025
Nature Methods

Volume: 22, P: 2024-2027
Clustering predicted structures at the scale of the known protein universe

The novel Foldseek clustering algorithm defines 2.30 million clusters of AlphaFold structures, identifying remote structural similarity of human immune-related proteins in prokaryotic species.

Inigo Barrio-Hernandez
Jingi Yeo
Martin Steinegger
ResearchOpen Access13 Sept 2023
Nature

Volume: 622, P: 637-645
Rapid and sensitive protein complex alignment with Foldseek-Multimer

Foldseek-Multimer offers a fast strategy for complex-to-complex alignment to quickly identify compatible sets of chain-to-chain alignments by their superpositions. It can compare billions of complex pairs in 11 h.

Woosub Kim
Milot Mirdita
Martin Steinegger
ResearchOpen Access05 Feb 2025
Nature Methods

Volume: 22, P: 469-472
Democratizing protein language model training, sharing and collaboration

SaprotHub is a community repository for protein language models.

Jin Su
Zhikai Li
Fajie Yuan
Research24 Oct 2025
Nature Biotechnology

P: 1-7
Fast and accurate protein structure search with Foldseek

Foldseek speeds up protein structural search by four to five orders of magnitude.

Michel van Kempen
Stephanie S. Kim
Martin Steinegger
ResearchOpen Access08 May 2023
Nature Biotechnology

Volume: 42, P: 243-246
Easy and accurate protein structure prediction using ColabFold

We describe the use of ColabFold to perform structure prediction of monomers, complexes and alternative conformations, either on the web or locally, and provide guidance on interpreting the results through confidence metrics and visualizations.

Gyuri Kim
Sewon Lee
Milot Mirdita
Protocols14 Oct 2024
Nature Protocols

Volume: 20, P: 620-642
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

The protein-level assembler can assemble protein catalogs from raw metagenomic sequencing data, enabling large-scale metagenomics studies.

Martin Steinegger
Milot Mirdita
Johannes Söding
Research24 Jun 2019
Nature Methods

Volume: 16, P: 603-606
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Chen Keasar
Liam J. McGuffin
Silvia N. Crivelli
ResearchOpen Access02 Jul 2018
Scientific Reports

Volume: 8, P: 1-18