DelPhiForce web server: electrostatic forces and energy calculations and visualization

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

doi:10.1093/bioinformatics/btx495

Cited by 42 publications

(49 citation statements)

References 11 publications

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“…This web server implements DelphiForce, which is a DelPhi‐based script, that allows one to calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, and so forth . Users can also generate vector representations of electrostatic force between the two objects.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, various methods, software, and webservers were developed utilizing DelPhi. These resources include changes of folding (SAAMBE method) and binding (SAAFEC and SAMPDI) free energies due to mutations, predicting nonspecifically bound ions (BION method), DelPhiPKa method and webservers for predicting pKa's in proteins, RNAs and DNAs, and calculating the electrostatic forces between macromolecules (DelPhiForce) …”

Section: Introductionmentioning

confidence: 99%

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DelPhi Suite: New Developments and Review of Functionalities

Jia

Chakravorty

et al. 2019

J Comput Chem

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Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object‐oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large‐scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DelPhi Suite: New Developments and Review of Functionalities

Jia

Chakravorty

et al. 2019

J Comput Chem

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“…To gather more information about the electrostatic interactions in dengue capsid, electrostatic binding forces in the four binding modes were calculated using DelPhiForce [27,28]. Each binding mode was manipulated by xing a heterotetramer and displacing the other one in a certain range of distance from 6Å to 40Å by intervals of 2Å, generating 12 modi ed structures.…”

Section: Delphiforce Calculationsmentioning

confidence: 99%

Using computational approaches to study dengue virus capsid assembly

Saucedo

Lopez

Jiadi

et al. 2019

Computational and Mathematical Biophysics

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Dengue viral capsid plays a significant role in viral life cycle of dengue, especially in vial genome protection and virus-cell fusion. Revealing mechanisms of the viral capsid protein assembly may lead to the discovery of anti-viral drugs that inhibit the assembly of the viral capsid. The E and M-proteins are arranged into heterotetramers, which consists of two copies of E and M-protein. The heterotetramers are assembled into a highly ordered capsid. While many investigations of the interactions between E and M-proteins have been performed, there are very few studies on the interactions between the heterotetramers and their roles in capsid assembly. Utilizing a series of computational approaches, this study focuses on the assembly mechanism of the heterotetramers. Our electrostatic analyses lead to the identification of four binding modes between each two dengue heterotetramers that repeat periodically throughout the virus capsid. Among these four binding modes, heterotetramers in binding modes I, II and IV are attractive. But in the binding mode III the heterotetramers repel each other, making mode III a suitable target for drug design. Furthermore, MD simulations were performed following by salt bridges analysis. This study demonstrates that using computational approaches is a promising direction to study the dengue virus.

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“…73 There are no many resources available for modeling electrostatic forces in molecular biology with the prominent exception of DelPhiForce. 74,75 This tool allows for modeling the electrostatic forces acting on individual atom(s), residue(s) or molecular partners. Thus, by comparing the forces within wild type residues and mutant, one can see the di®erences and attribute them to the e®ect of these di®erences on the functionality of the corresponding molecule.…”

Section: Electrostatic Forcesmentioning

confidence: 99%

Computational chemistry methods to investigate the effects caused by DNA variants linked with disease

Koirala

Alexov

2019

J. Theor. Comput. Chem.

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Computational chemistry offers variety of tools to study properties of biological macromolecules. These tools vary in terms of levels of details from quantum mechanical treatment to numerous macroscopic approaches. Here, we provide a review of computational chemistry algorithms and tools for modeling the effects of genetic variations and their association with diseases. Particular emphasis is given on modeling the effects of missense mutations on stability, conformational dynamics, binding, hydrogen bond network, salt bridges, and pH-dependent properties of the corresponding macromolecules. It is outlined that the disease may be caused by alteration of one or several of above-mentioned biophysical characteristics, and a successful prediction of pathogenicity requires detailed analysis of how the alterations affect the function of involved macromolecules. The review provides a short list of most commonly used algorithms to predict the molecular effects of mutations as well.

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DelPhiForce web server: electrostatic forces and energy calculations and visualization

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 42 publications

References 11 publications

DelPhi Suite: New Developments and Review of Functionalities

DelPhi Suite: New Developments and Review of Functionalities

Using computational approaches to study dengue virus capsid assembly

Computational chemistry methods to investigate the effects caused by DNA variants linked with disease

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