Journal ArticleDOI
Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide
TLDR
The cysteine protease model from X. campestris having similarity with human cathepsin B crystal structure may be used as an alternate approach to cleave Aβ peptide a causative agent of Alzheimer's disease.About:
This article is published in Computers in Biology and Medicine.The article was published on 2013-12-01. It has received 44 citations till now. The article focuses on the topics: Cysteine protease & Cathepsin B.read more
Citations
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Amyloid cascade hypothesis: Pathogenesis and therapeutic strategies in Alzheimer's disease.
TL;DR: This review critically evaluates general biochemical and physiological functions of Aβ directed therapeutics and their relevance and concludes that current research progress in several areas of therapies shall provide an effective treatment to cure this devastating disease.
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Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders
TL;DR: Computer-Aided Drug Design can assist researchers studying interactions between drugs and receptors and its applications towards the discovery of new drug candidates against various fatal NDs.
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In Silico Studies in Drug Research Against Neurodegenerative Diseases.
TL;DR: Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins involved in the development of a disease is recommended in future.
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Molecular Docking in Formulation and Development
TL;DR: This review summarizes recent findings of critical role played by molecular docking in the process of drug discovery and development and concludes the application of docking approach will assist to design a dosage form in the most cost effective and time saving manner.
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Insights into the molecular interactions between aminopeptidase and amyloid beta peptide using molecular modeling techniques.
TL;DR: The three-dimensional model of aminopeptidase (SGAK) using SWISS-MODEL, Geno3D and MODELLER revealed that amino acid Glu139 of SGAK might play an important role to degrade Aβ peptides, a causative agent of Alzheimer’s disease.
References
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VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
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A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.