ReviewProteins2015
Computational modeling of membrane proteins.
Review in Proteins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- Probing the binding stability of organic UV filters to human SLC transporters using AlphaFold and molecular dynamics simulations.Scientific reports · 2026Article
- Review
- Phylogenetic and Structural Analyses of Vesicular Glutamate Transporters.Molecular neurobiology · 2025Article
- Oversized nanodiscs for combined structural and functional investigation of multicomponent membrane protein systems.Scientific reports · 2025Article
- Nanobodies: From Discovery to AI-Driven Design.Biology · 2025Review
- A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Challenges of Protein-Protein Docking of the Membrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?Nano today · 2022Article
- Endogenous ion channels expressed in human embryonic kidney (HEK-293) cells.Pflugers Archiv : European journal of physiology · 2022Review
- Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor.BMC bioinformatics · 2021Article
- CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins.Journal of proteome research · 2021Article
- Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.Protein science : a publication of the Protein Society · 2021Article
- Genome-scale metabolic modeling reveals key features of a minimal gene set.Molecular systems biology · 2021Article
- Prediction of amphipathic helix-membrane interactions with Rosetta.PLoS computational biology · 2021Article
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Membrane Protein Engineering with Rosetta.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Integrative modeling of membrane-associated protein assemblies.Nature communications · 2020Article
- Short Disordered Epitope of CRTAM Ig-Like V Domain as a Potential Target for Blocking Antibodies.International journal of molecular sciences · 2020Article
- Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.Developmental cell · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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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.