Surface Generalized Born Method:  A Simple, Fast, and Precise Implicit Solvent Model beyond the Coulomb Approximation

Romanov, A. N.; Jabin, Sergey N.; Martynov, Y.B.; Сулимов, А. В.; Grigoriev, F. V.; Сулимов, В. Б.

doi:10.1021/jp046721s

Cited by 60 publications

(67 citation statements)

References 14 publications

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“…The binding energy dierence for the two dierent solvent models is insignicant for the majority of the complexes and is equal to several kcal/mol (see the Table 3), although for some complexes this dierence can reach 10 kcal/mol. So, it is possible to use the SGB [18,19] solvent model during the docking procedure which faster Âåñòíèê ÞÓðÃÓ. Ñåðèÿ ≪Ìàòåìàòè÷åñêîå ìîäåëèðîâàíèå è ïðîãðàììèðîâàíèå≫ (Âåñòíèê ÞÓðÃÓ ÌÌÏ).…”

Section: Resultsmentioning

confidence: 99%

“…Ñ. 94107 Table 3 The protein-ligand binding energy ∆G in kcal/mol, calculated by equation (1) in MMFF94 force eld in vacuum and for the two solvent models SGB [18,19] and PCM [20,21] than PCM [20,21], but less accurate. Although the solvent consideration decreases notably the binding energy dierences for the dierent hydrogen incorporation methods (see Table 3), though the binding energy can still vary from a few kcal/mol up to 10 20 kcal/mol.…”

Section: Resultsmentioning

confidence: 99%

“…It is also shown that the dierence in binding energies when using two implicit solvent models, SGB [18,19] and PCM [20,21] is only a few kcal/mol for most of the complexes. So, for the future docking programs with solvent accounting it is possible to use the SGB solvent model which is faster than the PCM one.…”

Section: Discussionmentioning

confidence: 99%

“…Interaction with water solvent is described in the frame of two implicit (continual) models: the Surface Generalized Born model (SGB) [18] implemented in the program DISOLV [19] and the Polarized Continuum Model (PCM) [20,21]. The complex and the ligand conformations obtained during the vacuum optimization are used for the energy calculation in solvent without their additional optimization.…”

Section: The Calculation Of Protein-ligand Binding Energymentioning

confidence: 99%

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Influence of the Method of Hydrogen Atoms Incorporation Into the Target Protein on the Protein-Ligand Binding Energy

Kutov¹,

Каткова²,

Сулимов³

et al. 2017

Bulletin of the SUSU. MMP

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Preparation of the target-protein, particularly the protein protonation method can affect considerably the spatial arrangement of the attached hydrogen atoms and the charge state of individual molecular groups in amino acid residues. This means that the calculated protein-ligand binding energies can vary signicantly depending on the method of the protein preparation, and it also can lead to the dierent docked positions of the ligand in the case of docking (positioning of the ligand in the protein active site). This work investigates the eect of the hydrogen atoms arrangement method in the targetprotein on the protein-ligand binding energy. All hydrogen atoms of target-protein are xed or movable. The comparison of the protein-ligand binding energies obtained for the test set of target-proteins prepared using six dierent programs is performed and it is shown that the protein-ligand binding energy depends signicantly on the method of hydrogen atoms incorporation, and dierences can reach 100 kcal/mol. It is also shown that taking into account solvent in the frame of one of the two continuum implicit models smooths out these dierences, but they are still about 10 − 20 kcal/mol. Moreover, we carried out the docking of the crystallized (native) ligands from the protein-ligand complexes using the SOL program and showed that the dierent methods of the hydrogen atoms addition to the protein can give signicantly dierent results both for the positioning of the native ligand and for its protein-ligand binding energy.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: The Calculation Of Protein-ligand Binding Energymentioning

confidence: 99%

See 2 more Smart Citations

Influence of the Method of Hydrogen Atoms Incorporation Into the Target Protein on the Protein-Ligand Binding Energy

Kutov¹,

Каткова²,

Сулимов³

et al. 2017

Bulletin of the SUSU. MMP

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show abstract

“…In GB, the electrostatic solvation energy is given by a sum of pairwise interactions between the solute atoms using the so-called effective Born radii of individual atoms to take into account the polarization effects of the bulk solvent. Since the work of Still et al, many studies have been reported on Born radius expressions, [20][21][22][23][24][25][26][27] fast numerical a) Electronic mail: xuzl@sjtu.edu.cn. b) Electronic mail: chengx@ornl.gov.…”

Section: Introductionmentioning

confidence: 99%

Treecode-based generalized Born method

Cheng

Yang

2011

The Journal of Chemical Physics

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We have developed a treecode-based O(N log N ) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

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Continuum Electrostatics Solvent Modeling with the Generalized Born Model

Onufriev

2010

Modeling Solvent Environments

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Surface Generalized Born Method: A Simple, Fast, and Precise Implicit Solvent Model beyond the Coulomb Approximation

Cited by 60 publications

References 14 publications

Influence of the Method of Hydrogen Atoms Incorporation Into the Target Protein on the Protein-Ligand Binding Energy

Influence of the Method of Hydrogen Atoms Incorporation Into the Target Protein on the Protein-Ligand Binding Energy

Treecode-based generalized Born method

Continuum Electrostatics Solvent Modeling with the Generalized Born Model

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