Computational Drug Discovery and Design
3.6 Dissecting A3D Performance and Applicability When compared with intrinsically disordered proteins or short peptides, which a ...
The capacity A3D to quickly generate mutated versions of a given structure with the mutation tool is according to our records th ...
In conclusion, A3D is an extremely versatile tool which aims to approximate protein aggregation propensities in physiological-li ...
buried regions may become reexposed and overestimated; (2) apolar stretches that were protected by nearby structural gatekeepers ...
might result into slight differences between initial entries and introduce a bias on the predictions. When a mutation is mod- el ...
Mckinnon C, Tabrizi SJ (2014) The ubiquitin- proteasome system in neurodegeneration. Antioxid Redox Signal 5:1–61 Wang G, Fersh ...
Pulido P, Llamas E, Llorente B, Ventura S, Wright LP, Rodrı ́guez-Concepcio ́n M (2016) Specific Hsp100 chaperones determine th ...
Chapter 22 Computational Analysis of Solvent Inclusion in Docking Studies of Protein–Glycosaminoglycan Systems Sergey A. Samsono ...
improve their performance [9–11], there is a persisting challenge to predict proper positions of water molecules on the surface ...
of steepest descent, conjugate gradient, and truncated Newton methods using 0.01 A ̊ RMSD for convergence criteria) [15] (seeNot ...
The most energetically favorable positions based on the visual inspection of GRID-calculated isosurfaces are used to place water ...
To set up a DMD experiment structures of the receptor and the ligand in one of the standard molecular formats are required. In ...
of the restraint is constant, and the restraint is applied to the distance between C and L atoms. Beside this additional restrai ...
placement predictions or returned “in place” after the water placement is accomplished. Then, the water molecules over- lapping ...
binding regions) are required in order not to neglect the solu- tions located on the borders of the chosen segments. Normally, ...
computational expenses and to slowing down the performance substantially. These values ofkandttMDwere calibrated for GAGs of le ...
References Esko JD, Kimata K, Lindahl U (2009) Proteo- glycans and sulfated glycosaminoglycans. In: Varki A, Cummings RD, Esko ...
Chapter 23 Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discover ...
the functional role of biomolecules. One of the transmembrane (TM) proteins, such as G protein-coupled receptors (GPCRs), provid ...
utilized to explore various aspects of proteins, such as protein structure plasticity, domain folding, identification of key res ...
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