ArticleNucleic acids research2017
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Application of Computational Techniques in Antibody Fc-Fused Molecule Design for Therapeutics.Molecular biotechnology · 2024Review
- Accelerating crystal structure determination with iterative AlphaFold prediction.Acta crystallographica. Section D, Structural biology · 2023Article
- The chemistry of snake venom and its medicinal potential.Nature reviews. Chemistry · 2022Review
- Implications of AlphaFold2 for crystallographic phasing by molecular replacement.Acta crystallographica. Section D, Structural biology · 2022Review
- Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evidence for the Involvement of Pleckstrin Homology Domain-Containing Proteins in the Transport of Enterocin DD14 (EntDD14); a Leaderless Two-Peptide Bacteriocin.International journal of molecular sciences · 2021Article
- Accurate prediction of protein structures and interactions using a three-track neural network.Science (New York, N.Y.) · 2021Article
- The coordination of major events in CScientific reports · 2021Article
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- Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.Scientific reports · 2020Article
- TheInternational journal of molecular sciences · 2020Article
- Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism.The Journal of biological chemistry · 2020Article
- A novel de novo nonsense mutation in ZC4H2 causes Wieacker-Wolff Syndrome.Molecular genetics & genomic medicine · 2020Article
- Computational Analysis ofCancer informatics · 2020Article
- Evaluation of template-based modeling in CASP13.Proteins · 2019Article
- I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future generations computer systems : FGCS · 2019Article
- Article
- MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.Acta crystallographica. Section D, Structural biology · 2018Article
- Use of designed sequences in protein structure recognition.Biology direct · 2018Article
- MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins.Nucleic acids research · 2018Article
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4 authors.
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Abstract
Molecular replacement (MR) is one of the most common techniques used for solving the phase problem in X-ray crystal diffraction. The success rate of MR however drops quickly when the sequence identity between query and templates is reduced, while the I-TASSER-MR server is designed to solve the phase problem for proteins that lack close homologous templates. Starting from a sequence, it first generates full-length models using I-TASSER by iterative structural fragment reassembly. A progressive sequence truncation procedure is then used for editing the models based on local variations of the structural assembly simulations. Next, the edited models are submitted to MR-REX to search for optimal placements in the crystal unit-cells through replica-exchange Monte Carlo simulations, with the phasing results used by CNS for final atomic model refinement and selection. The I-TASSER-MR algorithm was tested in large-scale benchmark datasets and solved 36% more targets compared to using the best threading templates. The server takes primary sequence and raw crystal diffraction data as input, with output containing annotated phase information and refined structure models. It also allows users to choose between different methods for setting B-factors and the number of models used for phasing. The online server is freely available at http://zhanglab.ccmb.med.umich.edu/I-TASSER-MR.
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