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Dr. Chandra Verma
Principal Investigator
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| Group Members |
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| Name | Title |
| Dr. Chandra VERMA |
Principal Investigator |
| Dr. Amor A. SAN JUAN |
Postdoctoral Fellow |
| Dr. ARUMUGAM Madhumalar |
Postdoctoral Fellow |
| Dr. RAGHUNATHAN Devanathan |
Postdoctoral Fellow |
| Dr. Shubhra GHOSH DASTIDAR |
Postdoctoral Fellow |
| Dr. SMITH Derek |
Postdoctoral Fellow |
| Dr. Thomas Leonard JOSEPH |
Postdoctoral Fellow |
| Ms. LOW Soo Mei |
Research Associate |
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Research Overview
A combination of homology modeling, electrostatic analyses, molecular dynamics simulations, normal mode analyses, reaction path methods and virtual screening through filtering and docking are used to understand the nature of proteins and their interactions with other proteins, nucleic acids or small molecules. The work builds upon foundations that are rooted in rigorous computational biochemistry benchmarked extensively against available experimental data (see for example previous work at http://www.ysbl.york.ac.uk/~chandra/reaction1.html & http://www.ysbl.york.ac.uk/~chandra/reaction2.html), and is now extended to problems that address biological issues. In particular we combine simulations with detailed experimental information to provide incisive insights into biology at an atomic level (EMBO Reports 9:144; 2008).
Our current research focus is on the p53 pathway, kinases, translation initiation, cyclins, defensins and basic structural/computational biophysical chemistry.
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| More Details |
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| Selected Publications |
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- Dodson GG, Lane DP, Verma CS.
Molecular simulations of protein dynamics: new windows on mechanisms in biology.
EMBO Rep. 2008 Feb;9(2):144-50.
PMID: 18246106 [PubMed - in process]
- Gul S, Hussain S, Thomas MP, Resmini M, Verma CS, Thomas EW, Brocklehurst K.
Generation of Nucleophilic Character in the Cys25/His159 Ion Pair of Papain Involves Trp177 but Not Asp158.
Biochemistry. 2008 Feb 19;47(7):2025-2035. Epub 2008 Jan 29.
PMID: 18225918 [PubMed - as supplied by publisher]
- Dey A, Verma CS, Lane DP.
Updates on p53: modulation of p53 degradation as a therapeutic approach.
Br J Cancer. 2008 Jan 15;98(1):4-8. Epub 2008 Jan 8.
PMID: 18182973 [PubMed - in process]
- Lee HJ, Srinivasan D, Coomber D, Lane DP, Verma CS.
Modulation of the p53-MDM2 interaction by phosphorylation of Thr18: a computational study.
Cell Cycle. 2007 Aug;6(21):2604-11. Epub 2007 Aug 20.
PMID: 17957142 [PubMed - indexed for MEDLINE]
- Lee HJ, Chua GH, Krishnan A, Lane DP, Verma CS.
Substrate specificity of cyclins determined by electrostatics.
Cell Cycle. 2007 Jul;6(18):2219-26. Epub 2007 Jul 6.
PMID: 17890901 [PubMed - indexed for MEDLINE]
- Verma C, Seebah S, Low SM, Zhou L, Liu SP, Li J, Beuerman RW.
Defensins: antimicrobial peptides for therapeutic development.
Biotechnol J. 2007 Nov;2(11):1353-9. Review.
PMID: 17886240 [PubMed - indexed for MEDLINE]
- Somani S, Chng CP, Verma CS.
Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
Proteins. 2007 Jun 1;67(4):868-85.
PMID: 17380484 [PubMed - indexed for MEDLINE]
- Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, Chuon D, Beuerman R, Verma C.
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides.
Nucleic Acids Res. 2007 Jan;35(Database issue):D265-8. Epub 2006 Nov 7.
PMID: 17090586 [PubMed - indexed for MEDLINE]
- Suresh A, Verma C.
Modelling study of dimerization in mammalian defensins.
BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S17.
PMID: 17254301 [PubMed - indexed for MEDLINE]
- Yeong SS, Zhu Y, Smith D, Verma C, Lim WG, Tan BJ, Li QT, Cheung NS, Cai M, Zhu YZ, Zhou SF, Tan SL, Duan W.
The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase Calpha.
J Biol Chem. 2006 Oct 13;281(41):30768-81. Epub 2006 Aug 8.
PMID: 16895917 [PubMed - indexed for MEDLINE]
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