Paper Search Console

Home Search Page About Contact

Journal Title

Title of Journal: J Mol Model

Search In Journal Title:

Abbravation: Journal of Molecular Modeling

Search In Journal Abbravation:

Publisher

Springer Berlin Heidelberg

Search In Publisher:

ISSN

0948-5023

Search In ISSN:
Search In Title Of Papers:

Homology modeling substrate docking and molecula

Authors: Shainaba A Saadhali Sameer Hassan Luke Elizabeth Hanna Uma Devi Ranganathan Vanaja Kumar
Publish Date: 2016/07/13
Volume: 22, Issue: 8, Pages: 180-
PDF Link

Abstract

Mycobacteriophages produce lysins that break down the host cell wall at the end of lytic cycle to release their progenies The ability to lyse mycobacterial cells makes the lysins significant Mycobacteriophage Che12 is the first reported temperate phage capable of infecting and lysogenising Mycobacterium tuberculosis Gp11 of Che12 was found to have Chitinase domain that serves as endolysin lysin A for Che12 Structure of gp11 was modeled and evaluated using Ramachandran plot in which 98  of the residues are in the favored and allowed regions Che12 lysin A was predicted to act on NAGNAMNAG molecules in the peptidoglycan of cell wall The tautomers of NAGNAMNAG molecule were generated and docked with lysin A The stability and binding affinity of lysin A – NAGNAMNAG tautomers were studied using molecular dynamics simulationsMs Shainaba A Saadhali is a recipient of Senior Research fellowship from Lady Tata Memorial Trust Mumbai India The authors would like to thank Dr P Velmurugan Head of the Department Department of Biophysics University of Madras Chennai India for his valuable suggestions The support and fund provided by National Institute for Research in Tuberculosis NIRT Chennai India is highly acknowledged The authors would like to thank Mr R Senthil Nathan NIRT Library for correcting the figures

Keywords:

References

.
Search In Abstract Of Papers:
Other Papers In This Journal:
  1. The X∙∙∙Au interactions in the CF 3 X (X = Cl, Br) ∙∙∙Au n ( n = 2, 3, and 4) complexes
  2. Structures and energies of the radicals and anions generated from chlorpyrifos
  3. Quantitative structure-activity relationship by CoMFA for cyclic urea and nonpeptide-cyclic cyanoguanidine derivatives on wild type and mutant HIV-1 protease
  4. The charge mobilities in fused ring Oligothiophenes and their derivatives: influence of molecular structures
  5. Computational design of a lipase for catalysis of the Diels-Alder reaction
  6. Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits
  7. Computational quest for spherical C 12 B 68 fullerenes with “ magic ” π-electrons and quasi-planar tetra-coordinated carbon
  8. The interaction strengths and spectroscopy parameters of the C 2 H 2 ∙∙∙HX and HCN∙∙∙HX complexes (X = F, Cl, CN, and CCH) and related ternary systems valued by fluxes of charge densities: QTAIM, CCFO, and NBO calculations
  9. Structure and properties of alizarin complex formed with alkali metal hydroxides in methanol solution
  10. Relationships between aqueous acidities and computed surface-electrostatic potentials and local ionization energies of substituted phenols and benzoic acids
  11. The simulation of UV spectroscopy and electronic analysis of temozolomide and dacarbazine chemical decomposition to their metabolites
  12. Cellular interaction through LewisX cluster: theoretical studies
  13. DFT tests for group 8 transition metal carbonyl complexes
  14. Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment
  15. Electronic, magnetic and optical properties of Cu, Ag, Au-doped Si clusters
  16. Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis
  17. Optical chemosensors for Cu(II) ion based on BODIPY derivatives: an experimental and theoretical study
  18. The interaction of CCl 4 with Ng (Ng = He, Ne, Ar), O 2 , D 2 O and ND 3 : rovibrational energies, spectroscopic constants and theoretical calculations
  19. Novel insights into the structural requirements for the design of selective and specific aldose reductase inhibitors
  20. Atomistic simulations of materials for optical chemical sensors: DFT-D calculations of molecular interactions between gas-phase analyte molecules and simple substrate models
  21. A theoretical investigation of the energetics and spectroscopic properties of the gas-phase linear proton-bound cation–molecule complexes, XCH + –N 2 (X = O, S)
  22. Computational study of graphene growth on copper by first-principles and kinetic Monte Carlo calculations
  23. Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking
  24. Comparison of the structural characteristics of Cu 2+ -bound and unbound α-syn12 peptide obtained in simulations using different force fields
  25. Improving the hydrogen storage properties of metal-organic framework by functionalization
  26. Mixtures of amino-acid based ionic liquids and water
  27. SWIFT MODELLER : A JAVA based GUI for molecular modeling
  28. Theoretical studies of the interaction between enflurane and water
  29. CNXeCl and CNXeBr species as halogen bond donors: a quantum chemical study on the structure, properties, and nature of halogen···nitrogen interactions
  30. Insights from comprehensive multiple receptor docking to HDAC8
  31. Molecular docking and molecular dynamics studies reveal structural basis of inhibition and selectivity of inhibitors EGCG and OSU-03012 toward glucose regulated protein-78 (GRP78) overexpressed in glioblastoma
  32. Computational investigation of stoichiometric effects, binding site heterogeneities, and selectivities of molecularly imprinted polymers
  33. Mechanism of OH-initiated atmospheric oxidation of E/Z-CF 3 CF = CFCF 3 : a quantum mechanical study
  34. Periodic density functional theory study of the high-pressure behavior of crystalline l -serine- l -ascorbic acid
  35. A model for the shuttle motions of puerarin and daidzin inside the cavity of β-cyclodextrin in aqueous acetic acid: insights from molecular dynamics simulations
  36. Mechanistic aspects of superacid mediated condensation of polyphenols with ketones. Implications for polymer synthesis
  37. Symmetric nested complexes of fullerenes
  38. A density functional study towards substituent effects on anion sensing with urea receptors
  39. An Insilico approach to High Altitude Pulmonary Edema - Molecular modeling of human β 2 adrenergic receptor and its interaction with Salmeterol & Nifedipine
  40. A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution
  41. The reaction mechanisms and kinetics of CF 3 CHFOCH 3 and CHF 2 CHFOCF 3 with atomic chlorine: a computational study
  42. Theoretical study of CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd and Ag)
  43. In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV
  44. Some molecular/crystalline factors that affect the sensitivities of energetic materials: molecular surface electrostatic potentials, lattice free space and maximum heat of detonation per unit volume
  45. Substitution, cooperative, and solvent effects on π pnicogen bonds in the FH 2 P and FH 2 As complexes
  46. Molecular crystals: the crystal field effect on molecular electronic structure
  47. Binuclear rhenium carbonyl nitrosyls related to dicobalt octacarbonyl and their decarbonylation products
  48. Evolution of the hydrogen-bonding motif in the melamine–cyanuric acid co-crystal: a topological study
  49. Structure-based characterization of the binding of peptide to the human endophilin-1 Src homology 3 domain using position-dependent noncovalent potential analysis
  50. Modeling of adsorption in nanopores
  51. A density functional theory study of hydrocarbon combustion and synthesis on Ni surfaces
  52. Catalytic mechanisms of Au 11 and Au 11-n Pt n ( n =1–2) clusters: a DFT investigation on the oxidation of CO by O 2
  53. Molecular modeling studies of poly lactic acid initiation mechanisms
  54. Dynamics of DNA polymerase I (Klenow fragment) under external force
  55. Comparative molecular field analysis and molecular dynamics studies of α/β hydrolase domain containing 6 (ABHD6) inhibitors
  56. Dyotropic rearrangement of bridgehead substituents in closed dithienylethenes; conjugated verses non-conjugated analogues
  57. A rational reduction of CI expansions: combining localized molecular orbitals and selected charge excitations
  58. A DFT investigation of conformational geometries and interconversion equilibria of phenylthiosemicarbazone and its complexation with zinc
  59. Molecular modeling of the GABA C receptor ligand-binding domain
  60. Photophysical properties of copper(I) complexes containing pyrazine-fused phenanthroline ligands: a joint experimental and theoretical investigation
  61. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A
  62. New pockets in dengue virus 2 surface identified by molecular dynamics simulation
  63. Study on the anisotropic response of condensed-phase RDX under repeated stress wave loading via ReaxFF molecular dynamics simulation
  64. Mechanism of extractive/oxidative desulfurization using the ionic liquid inimidazole acetate: a computational study
  65. Regression formulae for ab initio and density functional calculated chemical shifts
  66. Structural insights into human GPCR protein OA1: a computational perspective
  67. Performance of four different force fields for simulations of dipeptide conformations: GlyGly, GlyGly − , GlyGly · Cl − , GlyGly · Na + and GlyGly · (H 2 O) 2
  68. Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures
Search Result: