I-TASSER server: new development for protein structure and function predictions

By Jianyi Yang, Yang Zhang. 2015

2,240 citations recorded by the source corpus.

The I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER) is an online resource for automated protein structure prediction and structure-based function annotation. In I-TASSER, structural templates are first recognized from the PDB using multiple threading alignment approaches. Full-length structure models are then constructed by iterative fragment assembly simulations. The functional insights are finally derived by matching the predicted structure models with known proteins in the function databases. Although the server has been widely used for various biological and biomedical investigations, numerous comments and suggestions have been reported from the user community. In this article, we summarize recent developments on the I-TASSER server, which were designed to address the requirements from the user community and to increase the accuracy of modeling predictions. Focuses have been made on the introduction of new methods for atomic-level structure refinement, local structure quality estimation and biological function annotations. We expect that these new developments will improve the quality of the I-TASSER server and further facilitate its use by the community for high-resolution structure and function prediction.

Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Shape shifting: The multiple conformational substates of the PTEN N‐terminal PIP2 ‐binding domain (2022, methodology): “In previous work, we constructed a full-length model of PTEN21 using I-TASSER.22,23 Now, taking advantage of next-generation Deep Machine Learning methods, we have constructed full-length models of PTEN using AlphaFold224–26 and RoseTTAFold.27 Intriguingly, each of these methods predicted the PIP2-b”
Protein Structure and Function Prediction Using I-TASSER (2015, methodology): “The predicted structure and biological function are presented in the form of a Web page, the URL address of which is sent to the users by e-mail after the job is completed.”
Structural model of PORCN illuminates disease-associated variants and drug binding sites (2021, positive): “The C-terminal 40 amino acids of PORCN lack similarity to the other MBOATs and were therefore refined using I-TASSER, which is ideal for modeling sequences of low homology via thread methodology (see Methods) (Yang and Zhang, 2015a).”
Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, methodology): “In the absence of such a model, the method should be able to dock a homology modeled monomer (Eswar et al., 2006; Song et al., 2013; Yang and Zhang, 2015).”
Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 (2020, methodology): “The full‐length structure of SARS‐CoV‐2 spike glycoprotein was simulated by the I‐TASSER server online tool.(10) The spike‐ACE2 binding model was predicted using PRISM 2.”
Single-sequence protein structure prediction using language models and deep learning (2022, background): “An algorithm that predicts structure directly from a single sequence is—like energy-based folding engines 1–4 —closer to the real physical process than an algorithm that uses MSAs.”
In silico methods and tools for drug discovery (2021, methodology): “I-TASER I-TASER [144], Robetta server [145], and QUARK [146] are some of the available web servers for ab initio structure prediction.”