ArticlePLoS computational biology2017
Rosetta:MSF: a modular framework for multi-state computational protein design.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- ProDualNet: dual-target protein sequence design method based on protein language model and structure model.Briefings in bioinformatics · 2025Article
- Deep learning-guided design of dynamic proteins.Science (New York, N.Y.) · 2025Article
- Smad1 Promotes Tumorigenicity and Chemoresistance of Glioblastoma by Sequestering p300 From p53.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification.Nature communications · 2024Article
- A general computational design strategy for stabilizing viral class I fusion proteins.Nature communications · 2024Article
- Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
- ProRefiner: an entropy-based refining strategy for inverse protein folding with global graph attention.Nature communications · 2023Article
- Disentangling contact and ensemble epistasis in a riboswitch.Biophysical journal · 2023Article
- Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 ofComputational and structural biotechnology journal · 2023Article
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- The stability and dynamics of computationally designed proteins.Protein engineering, design & selection : PEDS · 2022Review
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
- Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol.Frontiers in immunology · 2022Article
- A rational blueprint for the design of chemically-controlled protein switches.Nature communications · 2021Article
- A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- PepFun: Open Source Protocols for Peptide-Related Computational Analysis.Molecules (Basel, Switzerland) · 2021Article
- Protein engineering for natural product biosynthesis and synthetic biology applications.Protein engineering, design & selection : PEDS · 2021Review
- Targeting galectin-3 with a high-affinity antibody for inhibition of high-grade serous ovarian cancer and other MUC16/CA-125-expressing malignancies.Scientific reports · 2021Article
- Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.Frontiers in molecular biosciences · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational protein design (CPD) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties. Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly specific tasks of protein engineering. Most of Rosetta's protocols optimize sequences based on a single conformation (i. e. design state). However, challenging CPD objectives like multi-specificity design or the concurrent consideration of positive and negative design goals demand the simultaneous assessment of multiple states. This is why we have developed the multi-state framework MSF that facilitates the implementation of Rosetta's single-state protocols in a multi-state environment and made available two frequently used protocols. Utilizing MSF, we demonstrated for one of these protocols that multi-state design yields a 15% higher performance than single-state design on a ligand-binding benchmark consisting of structural conformations. With this protocol, we designed de novo nine retro-aldolases on a conformational ensemble deduced from a (βα)8-barrel protein. All variants displayed measurable catalytic activity, testifying to a high success rate for this concept of multi-state enzyme design.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.