Software for molecular docking: a review
NS Pagadala, K Syed, J Tuszynski - Biophysical reviews, 2017 - Springer
Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …
of a target protein. As more protein structures are determined experimentally using X-ray …
The ClusPro web server for protein–protein docking
Abstract The ClusPro server (https://cluspro. org) is a widely used tool for protein–protein
docking. The server provides a simple home page for basic use, requiring only two files in …
docking. The server provides a simple home page for basic use, requiring only two files in …
[HTML][HTML] Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology
Cellular processes often depend on interactions between proteins and the formation of
macromolecular complexes. The impairment of such interactions can lead to deregulation of …
macromolecular complexes. The impairment of such interactions can lead to deregulation of …
HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy
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 …
biological processes. Determining the complex structures of these interactions is valuable, in …
Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies
C Schmidt, H Urlaub - Current opinion in structural biology, 2017 - Elsevier
Highlights•CX-MS identifies protein–protein interactions.•Cross-linking strategies targeting
different amino acids are available.•Combining CX-MS and cryo-EM delivers high-resolution …
different amino acids are available.•Combining CX-MS and cryo-EM delivers high-resolution …
New additions to the C lus P ro server motivated by CAPRI
The heavily used protein–protein docking server ClusPro performs three computational
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2
Trithorax-like group complex containing KDM6A acts antagonistically to Polycomb-
repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the …
repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the …
[PDF][PDF] Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1
J Bednar, I Garcia-Saez, R Boopathi, AR Cutter… - Molecular cell, 2017 - cell.com
Linker histones associate with nucleosomes to promote the formation of higher-order
chromatin structure, but the underlying molecular details are unclear. We investigated the …
chromatin structure, but the underlying molecular details are unclear. We investigated the …
Capturing protein communities by structural proteomics in a thermophilic eukaryote
The arrangement of proteins into complexes is a key organizational principle for many
cellular functions. Although the topology of many complexes has been systematically …
cellular functions. Although the topology of many complexes has been systematically …
Structural insights into the recognition of phosphorylated FUNDC1 by LC3B in mitophagy
Mitophagy is an essential intracellular process that eliminates dysfunctional mitochondria
and maintains cellular homeostasis. Mitophagy is regulated by the post-translational …
and maintains cellular homeostasis. Mitophagy is regulated by the post-translational …