The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes
J Mortier, C Rakers, M Bermudez, MS Murgueitio… - Drug discovery today, 2015 - Elsevier
Highlights•Which molecular dynamics (MD) techniques are available for drug design?•How
is MD used to investigate ligand–macromolecule complexes?•How are MD studies applied …
is MD used to investigate ligand–macromolecule complexes?•How are MD studies applied …
[HTML][HTML] Namdinator–automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
Model building into experimental maps is a key element of structural biology, but can be
both time consuming and error prone for low-resolution maps. Here we present Namdinator …
both time consuming and error prone for low-resolution maps. Here we present Namdinator …
Computational methodologies for real-space structural refinement of large macromolecular complexes
The rise of the computer as a powerful tool for model building and refinement has
revolutionized the field of structure determination for large biomolecular systems. Despite …
revolutionized the field of structure determination for large biomolecular systems. Despite …
Structure of the human 26S proteasome at a resolution of 3.9 Å
A Schweitzer, A Aufderheide… - Proceedings of the …, 2016 - National Acad Sciences
Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System
(UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically …
(UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically …
QwikMD—integrative molecular dynamics toolkit for novices and experts
The proper functioning of biomolecules in living cells requires them to assume particular
structures and to undergo conformational changes. Both biomolecular structure and motion …
structures and to undergo conformational changes. Both biomolecular structure and motion …
Structural insights into the functional cycle of the ATPase module of the 26S proteasome
M Wehmer, T Rudack, F Beck… - Proceedings of the …, 2017 - National Acad Sciences
In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated
degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP) …
degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP) …
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
Two structure determination methods, based on the molecular dynamics flexible fitting
(MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps …
(MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps …
Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site
The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and
regulates viral infectivity. Although the crystal structure of CypA in complex with the N …
regulates viral infectivity. Although the crystal structure of CypA in complex with the N …
Structure of native HIV-1 cores and their interactions with IP6 and CypA
The viral capsid plays essential roles in HIV replication and is a major platform engaging
host factors. To overcome challenges in study native capsid structure, we used the …
host factors. To overcome challenges in study native capsid structure, we used the …
Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
Abstract Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting
all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) …
all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) …