Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

SY Huang - Drug discovery today, 2014 - Elsevier
Highlights•Search strategies of current protein–protein docking algorithms were
reviewed.•Challenges and future directions of established approaches were discussed.•Post …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Y Yan, D Zhang, P Zhou, B Li… - Nucleic acids research, 2017 - academic.oup.com
Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of
biological processes. Determining the complex structures of these interactions is valuable, in …

Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

Y Yan, Z Wen, X Wang… - … : Structure, Function, and …, 2017 - Wiley Online Library
Protein–protein docking is an important computational tool for predicting protein–protein
interactions. With the rapid development of proteomics projects, more and more …

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

T Feng, F Chen, Y Kang, H Sun, H Liu, D Li… - Journal of …, 2017 - Springer
Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to
gain a deep understanding of many important biological functions in the living cells …

Modeling protein–protein or protein–DNA/RNA complexes using the HDOCK webserver

Y Yan, SY Huang - Protein Structure Prediction, 2020 - Springer
Protein–protein and protein–DNA/RNA interactions are involved in many cellular processes.
Therefore, determining their complex structures at the atomic level is valuable to gain …

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

C Yan, X Zou - Biophysical Journal, 2015 - cell.com
Short peptides play important roles in cellular processes including signal transduction,
immune response and transcription regulation. Correct identification of the peptide binding …

TRIC-A channel maintains store calcium handling by interacting with type 2 ryanodine receptor in cardiac muscle

X Zhou, KH Park, D Yamazaki, P Lin, M Nishi… - Circulation …, 2020 - Am Heart Assoc
Rationale: Trimeric intracellular cation (TRIC)-A and B are distributed to endoplasmic
reticulum/sarcoplasmic reticulum intracellular Ca2+ stores. The crystal structure of TRIC has …

Biomimetic polysaccharide-cloaked lipidic nanovesicles/microassemblies for improving the enzymatic activity and prolonging the action time for hyperuricemia …

L Yang, Y Zhang, J Xie, C Zhong, D He, T Wang, K Li… - Nanoscale, 2020 - pubs.rsc.org
The improvement and maintenance of enzymatic activities represent major challenges.
However, to address these we developed novel biomimetic polysaccharide hyaluronan (Hn) …