ReviewBiochemistry2016
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.
Review in Biochemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
119 citing papers in PubMed.
- Arrhythmia risk predictions from molecular simulations of cardiac ion channel-drug interactions.Biophysical journal · 2026Article
- Assessment of generative de novo peptide design methods for G protein-coupled receptors.PloS one · 2026Article
- Recent advances in the pharmacology of voltage-gated ion channels.Pharmacological reviews · 2025Review
- Large Library Docking and Biophysical Analysis of Small-Molecule TMPRSS2 Inhibitors.Journal of medicinal chemistry · 2025Article
- Targeting peptide antigens using a multiallelic MHC I-binding system.Nature biotechnology · 2025Article
- A Computationally Optimised Structural Integrity Sequence Enhances Vaccine Stability, Yield and Safety Profile.Research square · 2025Article
- Prediction of TdP Arrhythmia Risk Through Molecular Simulations of Conformation-specific Drug Interactions with the hERG KbioRxiv : the preprint server for biology · 2025Article
- Network Dynamics as Fingerprints of Thermostability in an In Silico-Engineered DyP-Type Peroxidase.ACS catalysis · 2025Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- Differentiating the solution structures and stability of transthyretin tetramer complexed with tolcapone and tafamidis using SEC-SWAXS and NMR.Journal of applied crystallography · 2025Article
- 6,7-Dichloro-1H-indole-2,3-dione-3-oxime functions as a superagonist for the intermediate-conductance CaMolecular pharmacology · 2025Article
- Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan.Journal of structural biology · 2025Article
- Structure-based computational design of antibody mimetics: challenges and perspectives.FEBS open bio · 2025Review
- Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.Nature chemical biology · 2025Article
- ProstaNet: A Novel Geometric Vector Perceptrons-Graph Neural Network Algorithm for Protein Stability Prediction in Single- and Multiple-Point Mutations with Experimental Validation.Research (Washington, D.C.) · 2025Article
- Atomistic mechanisms of the regulation of small-conductance CaProceedings of the National Academy of Sciences of the United States of America · 2024Article
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- Phase transition of GvpU regulates gas vesicle clustering in bacteria.Nature microbiology · 2024Article
- Sulfated disaccharide protects membrane and DNA damages from arginine-rich dipeptide repeats in ALS.Science advances · 2024Article
59 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
15 authors.
Funding
Abstract
Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987-2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3. Notable improvements include a substantially improved energy function, an XML-like language termed "RosettaScripts" for flexibly specifying modeling task, new analysis tools, the addition of the TopologyBroker to control conformational sampling, and support for multiple templates in comparative modeling. Rosetta's ability to model systems with symmetric proteins, membrane proteins, noncanonical amino acids, and RNA has also been greatly expanded and improved.
Indexed as
Identifiers
What OpenQuestion holds
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.