Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization.
By Dong Xu, Yang Zhang. 2011
1,008 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Mohammed Alquraishi
- Jianyi Yang
- Yang Zhang
- Chengxin Zhang
- S. Mortuza
- Baoji He
- Yanting Wang
- Robin Pearce
In Molecular Biology
- Yang Zhang
- Chengxin Zhang
- Mohammed Alquraishi
- Robin Pearce
- Jianyi Yang
- S. Mortuza
- Baoji He
- Yanting Wang
Citations in the corpus
- I-TASSER server: new development for protein structure and function predictions (2015, methodology): “To improve the local structure quality, we developed two algorithms, FG-MD (23) and ModRefiner (24).”
- 3DRobot: automated generation of diverse and well-packed protein structure decoys (2016, methodology): “, 2010)] can be significantly improved as demonstrated by the large-scale benchmark tests (Xu and Zhang, 2011).”
- GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors (2017, methodology): “Clashes between sidechains in the loops and the TMHs can be eliminated by carrying out energy minimization on the entire structure using, for example, the ModRefiner web server (30).”
- Single-sequence protein structure prediction using language models and deep learning (2022, methodology): “The remaining backbone and sidechain atoms are initially constructed using the unrefined full-atom model generated by ModRefiner 53 .”
- Protein Structure and Function Prediction Using I-TASSER (2015, methodology): “Starting from the SPICKER clusters, a second round of structure reassembly is performed to refine the structural models, with the low free-energy conformations refined by full-atomic simulations using FG-MD (Zhang et al., 2011) and ModRefiner (Xu and Zhang, 2011).”
- Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 (2017, methodology): “Here, the sequence-based contact restraints are not used, where the only external restraints in the ModRefiner and FG-MD simulations are those derived from the initial input models to the programs.”