ArticlePLoS computational biology2015
An Integrated Framework Advancing Membrane Protein Modeling and Design.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
What it found
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Who cites it
95 citing papers in PubMed, 183 citations in OpenAlex.
- Article
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- Energetic and structural control of polyspecificity in a multidrug transporter.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational modelling reveals novel insights into GnRH receptor activation and binding dynamics.Scientific reports · 2025Article
- S100A1ct: A Synthetic Peptide Derived From S100A1 Protein Improves Cardiac Performance and Survival in Preclinical Heart Failure Models.Circulation · 2025Article
- Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta.Journal of chemical theory and computation · 2024Article
- Accurate de novo design of heterochiral protein-protein interactions.Cell research · 2024Article
- Computational design of de novo bioenergetic membrane proteins.Biochemical Society transactions · 2024Review
- Article
- Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.bioRxiv : the preprint server for biology · 2024Article
- Deep mutational scanning reveals sequence to function constraints for SWEET family transporters.bioRxiv : the preprint server for biology · 2024Article
- Validation of de novo designed water-soluble and transmembrane β-barrels by in silico folding and melting.Protein science : a publication of the Protein Society · 2024Article
- De novo-designed transmembrane proteins bind and regulate a cytokine receptor.Nature chemical biology · 2024Article
- One-shot design elevates functional expression levels of a voltage-gated potassium channel.Protein science : a publication of the Protein Society · 2024Article
- Extracellular Kir2.1Circulation research · 2024Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Modeling membrane geometries implicitly in Rosetta.Protein science : a publication of the Protein Society · 2024Article
- Implicit model to capture electrostatic features of membrane environment.PLoS computational biology · 2024Article
- Transmembrane proteins in grape immunity: current knowledge and methodological advances.Frontiers in plant science · 2024Review
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and 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.