Molecular similarity based on electrostatic potential and electric field

Hodgkin, Edward E.; Richards, W. Graham

doi:10.1002/qua.560320814

Cited by 322 publications

(205 citation statements)

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“…First are the real-space measures that only refer to the density p. These include a residual (Jones, Zou, Cowan & Kjeldgaard, 1991) and a variety of differently normalized correlations (e.g. Zhang & Main, 1990;Carbo, Leyda & Arnau, 1980;Hodgkin & Richards, 1987). These measures are straightforward to implement and interpret, but it is difficult to see how they vary with resolution.…”

Section: Discussionmentioning

confidence: 99%

A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites

Gerstein¹

1992

Acta Cryst Sect A

109

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HANS GRIMMER 271 and the form of 7r given in Table 3 i.e. only the piezomagnetoelectric effect contributes to PI and P2. Also U2N2P, U2NES, Nb2C0409 and Nb2Mn409 have symmetry 3'm' according to Ole~ et al. (1976).The author is indebted to Professor H. Schmid for his suggestion to investigate the form of the piezomagnetoelectric effect and for stimulating discussions.References AIZU, K. (1970). Phys. Rev. B, 2, 754-772. GRIMMER, H. (1991a). Acta Cryst. A47, 226-232. GRIMMER, H. (1991b). Helv. Phys. Acta, 64, 187-188. KOPSKg, V. (1979 Resolution is a crucial parameter to consider in making surface comparisons. A method is presented here for the rapid, objective and automatic comparison of selected parts of protein surfaces as a function of resolution using differences and correlations of Fourier coefficients. A test-case application of this procedure to the surfaces of five immunoglobulin antigen-combining sites allowed them to be partitioned into two categories.

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Section: Discussionmentioning

confidence: 99%

A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites

Gerstein¹

1992

Acta Cryst Sect A

109

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“…Many methods use the fact that solutions to the PB equation away from the location of point charges are square-integrable [26] implying finite inner products: (1) and norms: (2) Similarity indices have been popular in QSAR studies [12,13,24] and the study of biomolecular electrostatics [53,8]. The most popular metrics were introduced by Hodgkin et al [24,12] and Carbo S C (u,v) [13]: (4) As can be seen from their definitions, these indices only differ by their choice of normalization; the Hodgkin index offers the advantage of distinguishing between functions which differ by a constant multiple, while the Carbo index provides a natural measure of the extent of orthogonality between two functions. In both cases, these indices are essentially modified L 2 (Ω) inner products which return 1 for identical functions, -1 for functions which are different only by a constant multiple of 1, and 0 for orthogonal (i.e., unrelated) functions.…”

Section: Similarity Index Methodsmentioning

confidence: 99%

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

Zhang¹,

Bajaj²,

Kwon³

et al. 2006

Multiscale Model. Simul.

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In this paper we present a method for the multi-resolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multi-resolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promises to perform well on future large-scale classification efforts across groups of structurally-diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally-relevant groups which demonstrate strong dependence on ligand binding sites. The results of the analyses are available from the linked web databases

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“…ASP is a software to calculate the similarity between two molecules originally developed by Burt and Richards [19]. The similarity index representing the nature of the amino acids was calculated as the Hodgkin similarity index [22] between the two amino acid residues. The Hodgkin index was initially developed starting from the Carbo Index [23], and accounts for the sign and magnitude of a property X of amino acids.…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Classification of proteins based on similarity of two-dimensional protein maps

Albrecht

Grant

Sisu

et al. 2008

Biophysical Chemistry

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Data reduction techniques are now a vital part of numerical analysis and principal component analysis is often used to identify important molecular features from a set of descriptors. We now take a different approach and apply data reduction techniques directly to protein structure. With this we can reduce the three-dimensional structural data into two-dimensions while preserving the correct relationships. With two-dimensional representations, structural comparisons between proteins are accelerated significantly. This means that protein-protein similarity comparisons are now feasible on a large scale. We show how the approach can help to predict the function of kinase structures according to the Hanks' classification based on their structural similarity to different kinase classes.

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Molecular similarity based on electrostatic potential and electric field

Abstract: A new definition of molecula similarity in terms of electron density is proposed and a method for calculating similarity based on molecular electrostatic potential and molecular electric field introduced. It is applied to some simple isosteres.

Cited by 322 publications

References 10 publications

A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites

A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

Classification of proteins based on similarity of two-dimensional protein maps

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