Results 21 to 30 of about 297,066 (279)

Improving macromolecular models of challenging ligands through combined QM/MM X-ray refinement [PDF]

Structural Dynamics
Conventional structural refinement relies on fixed stereochemical restraints for all components within the protein-ligand complex, using pre- determined parameters such as bond lengths, angles, and torsions in the unbound ligand conformation.
Margarita A Tararina, Lance M Westerhoff, Oleg Borbulevych, Matt Pokross, David A Critton   +4 more
doaj   +1 more source

A redetermination from the original data of the crystal structure of 2-amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate

Acta Crystallographica Section E: Crystallographic Communications, 2016
The title structure, C6H9.5N3O20.5+·C7H6.5NO20.5−, which might be named schematically as 2-amino-4,6-dimethoxypyrimidine-(μ2-hydrogen)-4-aminobenzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Muthiah &
Jan Fábry
doaj   +1 more source

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

PLoS Computational Biology, 2021
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates.
Jon Kapla, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent, Jens Carlsson   +4 more
doaj   +1 more source

Relational Concurrent Refinement: Timed Refinement [PDF]

, 2011
Data refinement in a state-based language such as Z is defined using a relational model in terms of the behaviour of abstract programs. Downward and upward simulation conditions form a sound and jointly complete methodology to verify relational data ...
Derrick, John, Eerke Boiten, Boiten, Eerke Albert, John Derrick, Boiten, Eerke   +4 more
core   +1 more source

Redetermination of cytosinium hydrogen maleate–cytosine (1/1) from the original data

Acta Crystallographica Section E: Crystallographic Communications, 2016
The title salt, C4H6N3O+·C4H3O4−·C4H5N3O, has been redetermined from the data published by Benali-Cherif, Falek & Direm [Acta Cryst. (2009), E65, o3058–o3059].
Jan Fábry
doaj   +1 more source

A long symmetric N...H...N hydrogen bond in bis(4-aminopyridinium)(1+) azide(1−): redetermination from the original data

Acta Crystallographica Section E: Crystallographic Communications, 2017
The structure of the title molecular salt, C10H13N4+·N3−, has been redetermined from the data published by Qian & Huang [Acta Cryst. (2010), E66, o3086; refcode WACMIY (Groom et al., 2016)].
Jan Fábry
doaj   +1 more source

Introducing extra operations in refinement [PDF]

, 2014
This paper reconsiders refinements which introduce actions on the concrete level which were not present at the abstract level. It considers a range of different basic refinement relations, covering the standard ones for formalisms like Event-B, Z ...
Boiten, Eerke Albert
core   +1 more source

Using the Quantum Interface in Phenix to improve and automate metal coordination in macromolecular models [PDF]

Structural Dynamics
Quantum Mechanical methods provide geometries and energies of molecules using just the atomic and electronic positions. Being independent of the experimental data, they provide complementary information.
Nigel W Moriarty
doaj   +1 more source

Towards biomarker-based optimization of deep brain stimulation in Parkinson’s disease patients

Frontiers in Neuroscience, 2023
BackgroundSubthalamic deep brain stimulation (DBS) is an established therapy to treat Parkinson’s disease (PD). To maximize therapeutic outcome, optimal DBS settings must be carefully selected for each patient.
Jana Peeters, Alexandra Boogers, Alexandra Boogers, Tine Van Bogaert, Till Anselm Dembek, Robin Gransier, Jan Wouters, Wim Vandenberghe, Wim Vandenberghe, Philippe De Vloo, Philippe De Vloo, Bart Nuttin, Bart Nuttin, Myles Mc Laughlin   +13 more
doaj   +1 more source

Relational Concurrent Refinement: Automata [PDF]

, 2009
Data refinement in a state-based language such as Z is defined using a relational model in terms of the behaviour of abstract programs. Downward and upward simulation conditions form a sound and jointly complete methodology to verify relational data ...
Derrick, John, Eerke Boiten, Boiten, Eerke Albert, Boiten, Eerke, John Derrick   +4 more
core   +1 more source