“…Additionally, testing with a range of filling ratio thresholds is also a good idea to distinguish the strength of different bound ions. With that said, we remark that the filling ratio should always be higher than 0.5; otherwise, a binding site would be treated as two binding sites and this would likely cause incorrect calculations [12] .…”
“…Additionally, testing with a range of filling ratio thresholds is also a good idea to distinguish the strength of different bound ions. With that said, we remark that the filling ratio should always be higher than 0.5; otherwise, a binding site would be treated as two binding sites and this would likely cause incorrect calculations [12] .…”
“…HIT uses the position information from explicit solvation simulations to calculate the ions occurrences to predict the binding sites. The process includes the preparation, initial, clustering, and optimal steps [16] . The preparation is to merge the frames of ions from the explicit MD simulation trajectory for analysis.…”
Section: Methodsmentioning
confidence: 99%
“…Then, the optimization calculated the mass center of the binding area and place-bound ions there. More details are shown in our previous software paper about hybridizing ions treatment method [16] . Fig.…”
Section: Methodsmentioning
confidence: 99%
“…These bound ions cannot be simulated by the current implicit models. Recently, we have developed a Hybridizing Ions Treatment (HIT) method [16] and applied it to a web server, which hybridizes the implicit solvent method with explicit ions to realistically calculate the electrostatic potential for highly charged biomolecules. It was proved that the hybrid method is more natural, accurate and reliable.…”
“…To overcome such limitations, a hybrid method involving DelPhi [ 48 , 49 , 50 , 51 ] (a popular Poisson–Boltzmann equation solver) and steered MD was developed. The method, termed DelPhi–Force MD (DFMD) [ 10 , 52 ], was successfully applied to dock substrates to an enzyme [ 2 ] and a biomolecule onto another biomolecule (such as barstar onto barnase) [ 10 ].…”
Section: Electrostatics Of Wild-type Biological Macromoleculesmentioning
This review outlines the role of electrostatics in computational molecular biophysics and its implication in altering wild-type characteristics of biological macromolecules, and thus the contribution of electrostatics to disease mechanisms. The work is not intended to review existing computational approaches or to propose further developments. Instead, it summarizes the outcomes of relevant studies and provides a generalized classification of major mechanisms that involve electrostatic effects in both wild-type and mutant biological macromolecules. It emphasizes the complex role of electrostatics in molecular biophysics, such that the long range of electrostatic interactions causes them to dominate all other forces at distances larger than several Angstroms, while at the same time, the alteration of short-range wild-type electrostatic pairwise interactions can have pronounced effects as well. Because of this dual nature of electrostatic interactions, being dominant at long-range and being very specific at short-range, their implications for wild-type structure and function are quite pronounced. Therefore, any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could be the dominant factor contributing to pathogenicity. However, we also outline that due to the plasticity of biological macromolecules, the effect of amino acid mutation may be reduced, and thus a charge deletion or insertion may not necessarily be deleterious.
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