Ultrafast shape recognition for similarity search in molecular databases

2007 ◽  
Vol 463 (2081) ◽  
pp. 1307-1321 ◽  
Author(s):  
Pedro J Ballester ◽  
W. Graham Richards
Keyword(s):  
Biological Activity ◽  
Three Dimensional ◽  
Molecular Shape ◽  
Scientific Disciplines ◽  
Distance Distributions ◽  
Molecular Databases ◽  
Hard Problems ◽  
Data Explosion ◽  
Novel Drug ◽  
Drug Leads

Molecular databases are routinely screened for compounds that most closely resemble a molecule of known biological activity to provide novel drug leads. It is widely believed that three-dimensional molecular shape is the most discriminating pattern for biological activity as it is directly related to the steep repulsive part of the interaction potential between the drug-like molecule and its macromolecular target. However, efficient comparison of molecular shape is currently a challenge. Here, we show that a new approach based on moments of distance distributions is able to recognize molecular shape at least three orders of magnitude faster than current methodologies. Such an ultrafast method permits the identification of similarly shaped compounds within the largest molecular databases. In addition, the problematic requirement of aligning molecules for comparison is circumvented, as the proposed distributions are independent of molecular orientation. Our methodology could be also adapted to tackle similar hard problems in other fields, such as designing content-based Internet search engines for three-dimensional geometrical objects or performing fast similarity comparisons between proteins. From a broader perspective, we anticipate that ultrafast pattern recognition will soon become not only useful, but also essential to address the data explosion currently experienced in most scientific disciplines.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

An Update on Recent Advances in Cubosome: A Novel Drug Delivery System

2021 ◽  
Vol 21 ◽  
Author(s):  
Madhukar Garg ◽  
Anju Goyal ◽  
Sapna Kumari
Keyword(s):  
Drug Delivery ◽  
Drug Delivery System ◽  
Lipid Bilayers ◽  
Delivery System ◽  
Liquid Crystalline ◽  
Three Dimensional ◽  
Biologically Active ◽  
Potential Applications ◽  
Health Related ◽  
Novel Drug

: Cubosomes are highly stable nanostructured liquid crystalline dosage delivery form derived from amphiphilic lipids and polymer-based stabilizers converting it in a form of effective biocompatible carrier for the drug delivery. The delivery form comprised of bicontinuous lipid bilayers arranged in three dimensional honeycombs like structure provided with two internal aqueous channels for incorporation of number of biologically active ingredients. In contrast liposomes they provide large surface area for incorporation of different types of ingredients. Due to the distinct advantages of biocompatibility and thermodynamic stability, cubosomes have remained the first preference as method of choice in the sustained release, controlled release and targeted release dosage forms as new drug delivery system for the better release of the drugs. As lot of advancement in the new form of dosage form has bring the novel avenues in drug delivery mechanisms so it was matter of worth to compile the latest updates on the various aspects of mentioned therapeutic delivery system including its structure, routes of applications along with the potential applications to encapsulate variety drugs to serve health related benefits.

scholarly journals Molecular Shape Descriptors. 2. Quantitative Structure-Activity Relationships Based Upon Three-Dimensional Molecular Shape Descriptor

1985 ◽  
Vol 40 (11) ◽  
pp. 1114-1120
Author(s):  
loan Motoc ◽  
Garland R. Marshall
Keyword(s):  
Enzyme Inhibitor ◽  
Three Dimensional ◽  
Shape Descriptor ◽  
Molecular Shape ◽  
Quantitative Structure Activity Relationship ◽  
Quantitative Structure ◽  
E Coli ◽  
Interactional Pattern ◽  
Structure Activity ◽  
Quantitative Structure Activity Relationships

A methodology to incorporate the three-dimensional molecular shape descriptor (3 D-MSD) into a quantitative structure-activity relationship is discussed in detail. The 3 D-MSD is calculated and correlated with Kiapp values for a set of 2,4-diamino-5-benzylpyrimidines which inhibit E. coli DHFR. The correlation (n = 22, r = 0.95, s = 0.214, F = 55.10) indicates that the polarization interaction dominates the enzyme-inhibitor interactional pattern.

scholarly journals Crystal structure of 5-[(4-carboxybenzyl)oxy]isophthalic acid

2016 ◽  
Vol 72 (8) ◽  
pp. 1219-1222
Author(s):  
Md. Serajul Haque Faizi ◽  
Musheer Ahmad ◽  
Akram Ali ◽  
Vadim A. Potaskalov
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Molecular Shape ◽  
Isophthalic Acid ◽  
Compound C ◽  
Dimensional Network ◽  
Benzene Rings

The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7)°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to thebcplane and enclosingR22(8) ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.

Epilogue

2016 ◽  
pp. 133-136
Author(s):  
William H. Brock
Keyword(s):  
Combinatorial Chemistry ◽  
Science And Technology ◽  
Three Dimensional ◽  
Structural Models ◽  
Service Science ◽  
Carbon Allotropes ◽  
Scientific Disciplines ◽  
Transdisciplinary Science ◽  
The 1960S

The Epilogue concludes with a brief look at some of the exciting, and more positive, aspects of chemistry since the 1960s: the use of computers to study perfect three-dimensional structural models and design new molecules on the screen; combinatorial chemistry; retrosynthesis; the discoveries of the carbon allotropes fullerene and graphene; and nanotechnology. In an age of cross-disciplinary, transdisciplinary science and technology several historians, sociologists, and philosophers of science have queried whether the concept of distinct scientific disciplines like chemistry, physics, and biology serves a purpose any longer. Has chemistry become a service science, or has chemistry taken over these other disciplines?

scholarly journals Phylogeny-Guided Selection of Priority Groups for Venom Bioprospecting: Harvesting Toxin Sequences in Tarantulas as a Case Study

Toxins ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 488 ◽  
Author(s):  
Tim Lüddecke ◽  
Andreas Vilcinskas ◽  
Sarah Lemke
Keyword(s):  
Success Rate ◽  
Mechanisms Of Action ◽  
Rational Selection ◽  
Almost All ◽  
Novel Drug ◽  
Drug Leads ◽  
Novel Structures ◽  
Animal Venoms ◽  
Selection Of

Animal venoms are promising sources of novel drug leads, but their translational potential is hampered by the low success rate of earlier biodiscovery programs, in part reflecting the narrow selection of targets for investigation. To increase the number of lead candidates, here we discuss a phylogeny-guided approach for the rational selection of venomous taxa, using tarantulas (family Theraphosidae) as a case study. We found that previous biodiscovery programs have prioritized the three subfamilies Ornithoctoninae, Selenocosmiinae, and Theraphosinae, which provide almost all of the toxin sequences currently available in public databases. The remaining subfamilies are poorly represented, if at all. These overlooked subfamilies include several that form entire clades of the theraphosid life tree, such as the subfamilies Eumenophorinae, Harpactirinae, and Stromatopelminae, indicating that biodiversity space has not been covered effectively for venom biodiscovery in Theraphosidae. Focusing on these underrepresented taxa will increase the likelihood that promising candidates with novel structures and mechanisms of action can be identified in future bioprospecting programs.

Molecular Shape Descriptors. 1. Three-Dimensional Molecular Shape Descriptor

1985 ◽  
Vol 40 (11) ◽  
pp. 1108-1113 ◽  
Author(s):  
I. Motoc ◽  
G. R. Marshall ◽  
R. A. Dammkoehler ◽  
J. Labanowski
Keyword(s):  
Numerical Integration ◽  
Van Der Waals ◽  
Three Dimensional ◽  
Shape Descriptor ◽  
Molecular Shape ◽  
Shape Descriptors ◽  
Van Der Waals Volume

The paper presents and illustrates a method which uses numerical integration of the van der Waals envelope(s) to calculate with desired accuracy the molecular van der Waals volume and the three-dimensional molecular shape descriptor defined as the twin-number [OV(α, β); NOV(β, α), where OV and NOV represent the overlapping and, respectively, the nonoverlapping van der Waals volumes of the molecules α and ß superimposed according to appropriate criteria.

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