scholarly journals EVR: Reconstruction of Bacterial Chromosome 3D Structure Using Error-Vector Resultant Algorithm

2018 ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Closed Loop ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Error Vector ◽  
3D Structures ◽  
Contact Frequency ◽  
Simple Error

ABSTRACTMore and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structures is an important task and in great need. We have developed a new reconstruction program for bacterial chromosome 3D structures called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

scholarly journals EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Parallel Implementation ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Computing Power ◽  
Error Vector ◽  
Contact Frequency ◽  
Simple Error

Abstract Background More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. Results We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. Conclusions EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

Sequence analysis, structure prediction of receptor proteins and In silico study of potential inhibitors for management of life threatening COVID-19

2021 ◽  
Vol 18 ◽  
Author(s):  
Hriday K. Basak ◽  
Soumen Saha ◽  
Joydeep Ghosh ◽  
Uttam Paswan ◽  
Sujoy Karmakar ◽  
...  
Keyword(s):  
Binding Site ◽  
Ursolic Acid ◽  
Density Functional ◽  
Actinomycin D ◽  
3D Structure ◽  
Natural Compounds ◽  
Surface Glycoprotein ◽  
Basis Set ◽  
3D Structures ◽  
Potential Inhibitors

Background: Treatment of the Covid-19 pandemic caused by the highly contagious and pathogenic SARS-CoV-2 is a global menace. Day by day this pandemic is getting worse. Doctors, Scientists and Researchers across the world are urgently scrambling for a cure for novel corona virus and continuously working at break neck speed to develop vaccine or drugs. But to date, there are no specific drugs or vaccine available in the market to cope up the virus. Objective: The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also to identify best natural compounds as potential inhibitors against COVID-19. Methods: The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool. Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study a small library of natural compounds (fifty compounds) was docked to the ACE2 binding site of the modelled surface glycoprotein of SARS-CoV-2 using Auto Dock Vina to repurpose these inhibitors for SARS-CoV-2. Conceptual density functional theory calculations of best eight compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and drug likeliness of the compounds were analyzed in the swissADME website. Results: In this study we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein and envelope protein obtained from different parts of the globe. We have modelled all the different sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular target which is essential for the development of therapeutics. Different electronic properties of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARS-CoV-2 showed that all the eight inhibitors (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here many folds better compared to hydroxychloroquine which has been found to be effective to treat patients suffering fromCOVID-19 pandemic. All the inhibitors meet most of criteria of drug likeness assessment. Conclusion: We will expect that eight compounds (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors against SARS-CoV-2.

scholarly journals Intrinsically Disordered Proteins in Chronic Diseases

Biomolecules ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 147 ◽  
Author(s):  
Prakash Kulkarni ◽  
Vladimir Uversky
Keyword(s):  
Chronic Diseases ◽  
Intrinsically Disordered Proteins ◽  
Large Fraction ◽  
3D Structure ◽  
Human Proteome ◽  
Disordered Proteins ◽  
3D Structures ◽  
Physiological Conditions ◽  
Intrinsically Disordered

It is now increasingly evident that a large fraction of the human proteome comprises proteins that, under physiological conditions, lack fixed, ordered 3D structures as a whole or have segments that are not likely to form a defined 3D structure [...]

Towards A 3D Chromosome Shape Alphabet

2020 ◽  
Author(s):  
Carlos Soto ◽  
Darshan Bryner ◽  
Nicola Neretti ◽  
Anuj Srivastava
Keyword(s):  
Structural Biology ◽  
3D Structure ◽  
Proof Of Concept ◽  
3D Structures ◽  
3 Dimensional ◽  
Topologically Associating Domains ◽  
Independent Test ◽  
Sequence Logos ◽  
Shape Data

AbstractThe study of the 3-dimensional (3D) structure of chromosomes – the largest macromolecules in biology – is one of the most challenging to date in structural biology. Here, we develop a novel representation of chromosomes, as sequences of shape letters from a finite shape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct a Chromosome Shape Alphabet (CSA) from an ensemble of chromosome 3D structures inferred from Hi-C data – via SIMBA3D or other methods – by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs’ 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form the Chromosome Shape Letters (CSLs) of the alphabet. We provide a proof-of-concept for these CSLs by reconstructing independent test curves using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize the variability of shapes in an ensemble of chromosome 3D structures using generalized sequence logos.

scholarly journals 3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction

2019 ◽  
Vol 20 (17) ◽  
pp. 4116 ◽  
Author(s):  
Jun Wang ◽  
Jian Wang ◽  
Yanzhao Huang ◽  
Yi Xiao
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Web Server ◽  
Structure Optimization ◽  
Optimization Procedure ◽  
Biological Functions ◽  
Rna Sequences ◽  
3D Structures ◽  
3D Structure Prediction ◽  
Sampling Structure

3D structures of RNAs are the basis for understanding their biological functions. However, experimentally solved RNA 3D structures are very limited in comparison with known RNA sequences up to now. Therefore, many computational methods have been proposed to solve this problem, including our 3dRNA. In recent years, 3dRNA has been greatly improved by adding several important features, including structure sampling, structure ranking and structure optimization under residue-residue restraints. Particularly, the optimization procedure with restraints enables 3dRNA to treat pseudoknots in a new way. These new features of 3dRNA can greatly promote its performance and have been integrated into the 3dRNA v2.0 web server. Here we introduce these new features in the 3dRNA v2.0 web server for the users.

scholarly journals VIRTUAL SCREENING OF HETEROCYCLIC COMPOUNDS AGAINST ANGIOTENSIN-CONVERTING ENZYME FOR POTENTIAL ANTIHYPERTENSIVE INHIBITORS

2019 ◽  
pp. 350-355
Author(s):  
ZOZIMUS DIVYA LOBO C ◽  
SYED MOHAMED A ◽  
GNANENDRA SHANMUGAM
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Ace Inhibitors ◽  
Heterocyclic Compounds ◽  
Density Functional ◽  
Energy Gap ◽  
3D Structure ◽  
Antihypertensive Activity ◽  
Converting Enzyme ◽  
Molecular Electronic ◽  
3D Structures

Objective: The objective of this study was to investigate the antihypertensive activity of heterocyclic compounds against angiotensin-converting enzyme (ACE) through molecular docking studies. Methods: The X-ray crystal three-dimensional (3D) structure of human ACE complexed with lisinopril (PDB ID: 1O86) was retrieved from protein databank. The two-dimensional structures of 10 selected heterocyclic compounds were drawn in ACD-Chemsketch and converted into 3D structures. The 3D structures of compounds were virtually screened in the binding pockets of ACE using FlexX docking program. Further, the chemical entities revealing the molecular electronic structures of the best docked compound (Compound-4) were explored through density functional theory studies. Results: The Compound-4 showed the highest docking score of −26.6290 kJ/mol with ACE. The Hbond and non-bonded interactions are favored by phenylalanine, leucine, and arginine. The energy gap of 1.60 eV between highest occupied molecular orbital and lowest unoccupied molecular orbitals explained the presence of strong electron-acceptor group. Furthermore, the molecular electrostatic potential studies clearly envisaged the requirement of electropositive and electronegative groups are crucial for the ACE inhibitor activities. Conclusion: The identification of good ACE inhibitors requires the understanding of the current ACE inhibitors. Thus, the docking interactions of Compound-4 and its molecular electronic structure significantly imply its potential as antihypertensive agent. However, further clinical studies are required to ascertain its potential toxic effects.

The function analysis diagram: Intended benefits and coexistence with other functional models

2013 ◽  
Vol 27 (3) ◽  
pp. 249-257 ◽  
Author(s):  
Marco Aurisicchio ◽  
Rob Bracewell ◽  
Gareth Armstrong
Keyword(s):  
Adaptive Design ◽  
Research Collaboration ◽  
Function Analysis ◽  
Software Tool ◽  
Major Power ◽  
Modeling Tools ◽  
Diagram Method ◽  
Functional Models ◽  
Simple Notation

AbstractUnderstanding product functions is a key aspect of the work undertaken by engineers involved in complex system design. The support offered to these engineers by existing modeling tools such as the function tree and the function structure is limited because they are not intuitive and do not scale well to deal with real-world engineering problems. A research collaboration between two universities and a major power system company in the aerospace domain has allowed the authors to further develop a method for function analysis known as function analysis diagram that was already in use by line engineers. The capability to generate and edit these diagrams was implemented in the Decision Rationale editor, a software tool for capturing design rationale. This article presents the intended benefits of the method and justifies them using an engineering case study. The results of the research have shown that the function analysis diagram method has a simple notation, permits the modeling of product functions together with structure, allows the generation of rich and accurate descriptions of product functionality, is useful to work with variant and adaptive design tasks, and can coexist with other functional modeling methods.

scholarly journals Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections

2019 ◽  
Vol 93 (7) ◽  
Author(s):  
Yuanzhu Gao ◽  
Shanshan Liu ◽  
Jiamiao Huang ◽  
Qianqian Wang ◽  
Kunpeng Li ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
3D Structure ◽  
Structural Features ◽  
Economic Losses ◽  
Scylla Paramamosain ◽  
Multiple Infections ◽  
Mud Crab ◽  
Cryo Electron Microscopy ◽  
Novel Virus ◽  
Icosahedral Capsid

ABSTRACT Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-Å resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-Å resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus. IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.

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