I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction
Most proteins in cells are composed of multiple folding units (or domains) to perform
complex functions in a cooperative manner. Relative to the rapid progress in single-domain …
complex functions in a cooperative manner. Relative to the rapid progress in single-domain …
[HTML][HTML] Homology modeling in the time of collective and artificial intelligence
Homology modeling is a method for building protein 3D structures using protein primary
sequence and utilizing prior knowledge gained from structural similarities with other …
sequence and utilizing prior knowledge gained from structural similarities with other …
[HTML][HTML] The structural coverage of the human proteome before and after AlphaFold
The protein structure field is experiencing a revolution. From the increased throughput of
techniques to determine experimental structures, to developments such as cryo-EM that …
techniques to determine experimental structures, to developments such as cryo-EM that …
Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning
Accurately capturing domain-domain interactions is key to understanding protein function
and designing structure-based drugs. Although AlphaFold2 has made a breakthrough on …
and designing structure-based drugs. Although AlphaFold2 has made a breakthrough on …
Assembling multidomain protein structures through analogous global structural alignments
Most proteins exist with multiple domains in cells for cooperative functionality. However,
structural biology and protein folding methods are often optimized for single-domain …
structural biology and protein folding methods are often optimized for single-domain …
Recent advances and challenges in protein structure prediction
Artificial intelligence has made significant advances in the field of protein structure prediction
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …
Enhanced GROMACS: toward a better numerical simulation framework
The GROMACS software package represented a promising direction toward the molecular
dynamic simulation and there is ongoing interest to extend it. In this study, we introduce a …
dynamic simulation and there is ongoing interest to extend it. In this study, we introduce a …
Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95
IS Yanez Orozco, FA Mindlin, J Ma, B Wang… - Nature …, 2018 - nature.com
Previous studies of the N-terminal PDZ tandem from PSD-95 produced divergent models
and failed to identify interdomain contacts stabilizing the structure. We used ensemble and …
and failed to identify interdomain contacts stabilizing the structure. We used ensemble and …
Reconstruction of coupled intra-and interdomain protein motion from nuclear and electron magnetic resonance
Proteins composed of multiple domains allow for structural heterogeneity and interdomain
dynamics that may be vital for function. Intradomain structures and dynamics can influence …
dynamics that may be vital for function. Intradomain structures and dynamics can influence …
Structural analogue-based protein structure domain assembly assisted by deep learning
Motivation With the breakthrough of AlphaFold2, the protein structure prediction problem has
made remarkable progress through deep learning end-to-end techniques, in which correct …
made remarkable progress through deep learning end-to-end techniques, in which correct …