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] Progress at protein structure prediction, as seen in CASP15
A Elofsson - Current Opinion in Structural Biology, 2023 - Elsevier
In Dec 2020, the results of AlphaFold version 2 were presented at CASP14, sparking a
revolution in the field of protein structure predictions. For the first time, a purely …
revolution in the field of protein structure predictions. For the first time, a purely …
I-TASSER server: new development for protein structure and function predictions
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 …
resource for automated protein structure prediction and structure-based function annotation …
Protein structure and function prediction using I‐TASSER
I‐TASSER is a hierarchical protocol for automated protein structure prediction and structure‐
based function annotation. Starting from the amino acid sequence of target proteins, I …
based function annotation. Starting from the amino acid sequence of target proteins, I …
Template-based protein structure modeling using the RaptorX web server
A key challenge of modern biology is to uncover the functional role of the protein entities that
compose cellular proteomes. To this end, the availability of reliable three-dimensional …
compose cellular proteomes. To this end, the availability of reliable three-dimensional …
I-TASSER: a unified platform for automated protein structure and function prediction
The iterative threading assembly refinement (I-TASSER) server is an integrated platform for
automated protein structure and function prediction based on the sequence-to-structure-to …
automated protein structure and function prediction based on the sequence-to-structure-to …
[HTML][HTML] Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene
MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end
stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes …
stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes …
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15
W Zheng, Q Wuyun, PL Freddolino… - … Structure, Function, and …, 2023 - Wiley Online Library
We report the results of the “UM‐TBM” and “Zheng” groups in CASP15 for protein monomer
and complex structure prediction. These prediction sets were obtained using the D‐I …
and complex structure prediction. These prediction sets were obtained using the D‐I …
[HTML][HTML] Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets
WP Feinstein, M Brylinski - Journal of cheminformatics, 2015 - Springer
Background Computational approaches have emerged as an instrumental methodology in
modern research. For example, virtual screening by molecular docking is routinely used in …
modern research. For example, virtual screening by molecular docking is routinely used in …
[HTML][HTML] Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
One of critical difficulties of molecular dynamics (MD) simulations in protein structure
refinement is that the physics-based energy landscape lacks a middle-range funnel to guide …
refinement is that the physics-based energy landscape lacks a middle-range funnel to guide …