Journal ArticleDOI
Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants.
Rituraj Purohit,R. Rajasekaran,C. Sudandiradoss,C. George Priya Doss,K. Ramanathan,Sethumadhavan Rao +5 more
TLDR
The results clearly suggest that Ritonavir is not able to appropriately bind at the active site of each HIV-1 protease mutant due to RMSD difference of the amino acid (Asp) at the position 25 of all mutants.About:
This article is published in International Journal of Biological Macromolecules.The article was published on 2008-05-01. It has received 36 citations till now. The article focuses on the topics: HIV-1 protease & HIV Protease Inhibitor.read more
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In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein
TL;DR: Differences in interaction and flexibility of interacting residues of mutant are mainly due to less involvement in formation of inter and intramolecular hydrogen bonds, which likely contribute to or represent novel mechanisms in laminopathy development.
Journal ArticleDOI
Drug resistance mechanism of PncA in Mycobacterium tuberculosis
TL;DR: An exhaustive analysis of the binding site flexibility and its 3D conformations that may serve as new starting points for structure-based drug design and helps the researchers to design new inhibitors with consideration of rigid criterion of binding residues due to mutation of this essential target.
Journal ArticleDOI
Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight
TL;DR: Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region and provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor.
Journal ArticleDOI
Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E.
Ambuj Kumar,Rituraj Purohit +1 more
TL;DR: This study provided a promising computational methodology to study the tumorigenic consequences of nsSNPs that have not been characterized and clear clue to the wet lab scientist.
Journal ArticleDOI
Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants
TL;DR: Insight is provided into the molecular basis of TMC-114 resistance major flap mutations (I50V and I54M) in HIV-1 protease and the shape complementarity and receptor-ligand interaction analysis supported by unrestrained all-atom molecular dynamics simulations of wild and major flap mutants ofAIDS protease that sample large conformational changes of the flaps and active site binding residues.
References
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Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
Nicolas Guex,Manuel C. Peitsch +1 more
TL;DR: An environment for comparative protein modeling is developed that consists of SWISS‐MODEL, a server for automated comparativeprotein modeling and of the SWiss‐PdbViewer, a sequence to structure workbench that provides a large selection of structure analysis and display tools.
Journal ArticleDOI
Viral dynamics in human immunodeficiency virus type 1 infection
Xiping Wei,Sajal Ghosh,Maria E. Taylor,Victoria A. Johnson,Emilio A. Emini,Deutsch Paul J,Jeffrey D. Lifson,Sebastian Bonhoeffer,Martin A. Nowak,Beatrice H. Hahn,Michael S. Saag,George M. Shaw +11 more
TL;DR: Almost complete replacement of wild-type virus in plasma by drug-resistant variants occurs after fourteen days, indicating that HIV-1 viraemia is sustained primarily by a dynamic process involving continuous rounds of de novo virus infection and replication and rapid cell turnover.
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Solvent-Accessible Surfaces of Proteins and Nucleic Acids
TL;DR: A method is presented for analytically calculating a smooth, three-dimensional contour about a molecule, which has been applied in enzymology, rational drug design, immunology, and understanding DNA base sequence recognition.