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Items: 1 to 50 of 112

1.

Conformational Transitions of Melittin between Aqueous and Lipid Phases: Comparison of Simulations with Experiments.

Fox SJ, Lakshminarayanan R, Beuerman RW, Li J, Verma CS.

J Phys Chem B. 2018 Sep 20;122(37):8698-8705. doi: 10.1021/acs.jpcb.8b06781. Epub 2018 Sep 10.

PMID:
30114909
2.

Molecular Insights into the Membrane Affinities of Model Hydrophobes.

Li J, Beuerman RW, Verma CS.

ACS Omega. 2018 Mar 31;3(3):2498-2507. doi: 10.1021/acsomega.7b01759. Epub 2018 Mar 1.

3.

Small Molecules Targeting the Inactive Form of the Mnk1/2 Kinases.

Kannan S, Pradhan MR, Cherian J, Joseph TL, Poh ZY, Hai Yan Y, Melvyn H, Boping L, Jeffrey H, Nacro K, Verma CS.

ACS Omega. 2017 Nov 30;2(11):7881-7891. doi: 10.1021/acsomega.7b01403. Epub 2017 Nov 14.

4.

Homologous Lympho-Epithelial Kazal-type Inhibitor Domains Delay Blood Coagulation by Inhibiting Factor X and XI with Differential Specificity.

Ramesh K, Lama D, Tan KW, Nguyen VS, Chew FT, Verma CS, Mok YK.

Structure. 2018 Sep 4;26(9):1178-1186.e3. doi: 10.1016/j.str.2018.05.018. Epub 2018 Jul 12.

PMID:
30017565
5.

Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide.

Liu BH, Jobichen C, Chia CSB, Chan THM, Tang JP, Chung TXY, Li J, Poulsen A, Hung AW, Koh-Stenta X, Tan YS, Verma CS, Tan HK, Wu CS, Li F, Hill J, Joy J, Yang H, Chai L, Sivaraman J, Tenen DG.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7119-E7128. doi: 10.1073/pnas.1801253115. Epub 2018 Jul 5.

PMID:
29976840
6.

A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes.

Marzinek JK, Bag N, Huber RG, Holdbrook DA, Wohland T, Verma CS, Bond PJ.

J Chem Theory Comput. 2018 Jul 10;14(7):3920-3932. doi: 10.1021/acs.jctc.8b00438. Epub 2018 Jun 20.

PMID:
29874075
7.

Optimization of Selective Mitogen-Activated Protein Kinase Interacting Kinases 1 and 2 Inhibitors for the Treatment of Blast Crisis Leukemia.

Yang H, Chennamaneni LR, Ho MWT, Ang SH, Tan ESW, Jeyaraj DA, Yeap YS, Liu B, Ong EH, Joy JK, Wee JLK, Kwek P, Retna P, Dinie N, Nguyen TTH, Tai SJ, Manoharan V, Pendharkar V, Low CB, Chew YS, Vuddagiri S, Sangthongpitag K, Choong ML, Lee MA, Kannan S, Verma CS, Poulsen A, Lim S, Chuah C, Ong TS, Hill J, Matter A, Nacro K.

J Med Chem. 2018 May 24;61(10):4348-4369. doi: 10.1021/acs.jmedchem.7b01714. Epub 2018 May 7.

PMID:
29683667
8.

Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds.

Kozic M, Fox SJ, Thomas JM, Verma CS, Rigden DJ.

Proteins. 2018 May;86(5):548-565. doi: 10.1002/prot.25473. Epub 2018 Feb 18.

PMID:
29388242
9.

Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53.

Chan JV, Ping Koh DX, Liu Y, Joseph TL, Lane DP, Verma CS, Tan YS.

Oncotarget. 2017 Dec 1;8(68):112825-112840. doi: 10.18632/oncotarget.22829. eCollection 2017 Dec 22.

10.

An intramolecular tryptophan-condensation approach for peptide stapling.

Hui EY, Rout B, Tan YS, Verma CS, Chan KP, Johannes CW.

Org Biomol Chem. 2018 Jan 17;16(3):389-392. doi: 10.1039/c7ob02667f.

PMID:
29271460
11.

Modeling the full length HIV-1 Gag polyprotein reveals the role of its p6 subunit in viral maturation and the effect of non-cleavage site mutations in protease drug resistance.

Su CT, Kwoh CK, Verma CS, Gan SK.

J Biomol Struct Dyn. 2017 Dec 27:1-12. doi: 10.1080/07391102.2017.1417160. [Epub ahead of print]

PMID:
29237328
12.

Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations.

Yadahalli S, Li J, Lane DP, Gosavi S, Verma CS.

Sci Rep. 2017 Nov 15;7(1):15600. doi: 10.1038/s41598-017-15930-4.

13.

A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein-protein interactions identifies a novel putative Mdm2-binding site in p53.

Wong JH, Alfatah M, Sin MF, Sim HM, Verma CS, Lane DP, Arumugam P.

BMC Biol. 2017 Nov 9;15(1):108. doi: 10.1186/s12915-017-0446-7.

14.

Correction to Probing the Binding Mechanism of Mnk Inhibitors by Docking and Molecular Dynamics Simulations.

Kannan S, Poulsen A, Yang HY, Ho M, Ang SH, Eldwin TSW, Jeyaraj DA, Chennamaneni LR, Liu B, Hill J, Verma CS, Nacro K.

Biochemistry. 2017 Nov 7;56(44):5964-5965. doi: 10.1021/acs.biochem.7b00996. No abstract available.

PMID:
29077411
15.

A New Generation of Arachidonic Acid Analogues as Potential Neurological Agent Targeting Cytosolic Phospholipase A2.

Ng CY, Kannan S, Chen YJ, Tan FCK, Ong WY, Go ML, Verma CS, Low CM, Lam Y.

Sci Rep. 2017 Oct 20;7(1):13683. doi: 10.1038/s41598-017-13996-8.

16.

Editorial.

Bond PJ, Verma CS.

Prog Biophys Mol Biol. 2017 Sep;128:1-2. doi: 10.1016/j.pbiomolbio.2017.07.005. No abstract available.

PMID:
28743422
17.

Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design.

Li J, Koh JJ, Liu S, Lakshminarayanan R, Verma CS, Beuerman RW.

Front Neurosci. 2017 Feb 14;11:73. doi: 10.3389/fnins.2017.00073. eCollection 2017. Review.

18.

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it.

Lua WH, Ling WL, Su CT, Yeo JY, Verma CS, Eisenhaber B, Eisenhaber F, Gan SK.

Cell Cycle. 2017 Mar 4;16(5):457-467. doi: 10.1080/15384101.2017.1281480. Epub 2017 Jan 19.

19.

Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041.

Tiwari G, Verma CS.

J Phys Chem B. 2017 Feb 2;121(4):657-670. doi: 10.1021/acs.jpcb.6b09900. Epub 2017 Jan 20.

PMID:
28048940
20.

Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer.

Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR.

Angew Chem Int Ed Engl. 2017 Jan 9;56(2):524-529. doi: 10.1002/anie.201609427. Epub 2016 Dec 5.

21.

Water-Bridge Mediates Recognition of mRNA Cap in eIF4E.

Lama D, Pradhan MR, Brown CJ, Eapen RS, Joseph TL, Kwoh CK, Lane DP, Verma CS.

Structure. 2017 Jan 3;25(1):188-194. doi: 10.1016/j.str.2016.11.006. Epub 2016 Dec 1.

22.

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

Tan YS, Reeks J, Brown CJ, Thean D, Ferrer Gago FJ, Yuen TY, Goh ET, Lee XE, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble ME, Verma CS.

J Phys Chem Lett. 2016 Sep 1;7(17):3452-7. doi: 10.1021/acs.jpclett.6b01525. Epub 2016 Aug 22.

23.

PDK1-SGK1 Signaling Sustains AKT-Independent mTORC1 Activation and Confers Resistance to PI3Kα Inhibition.

Castel P, Ellis H, Bago R, Toska E, Razavi P, Carmona FJ, Kannan S, Verma CS, Dickler M, Chandarlapaty S, Brogi E, Alessi DR, Baselga J, Scaltriti M.

Cancer Cell. 2016 Aug 8;30(2):229-242. doi: 10.1016/j.ccell.2016.06.004. Epub 2016 Jul 21.

24.

Stapled peptide design: principles and roles of computation.

Tan YS, Lane DP, Verma CS.

Drug Discov Today. 2016 Oct;21(10):1642-1653. doi: 10.1016/j.drudis.2016.06.012. Epub 2016 Jun 18. Review.

PMID:
27326912
25.

Branched Peptide, B2088, Disrupts the Supramolecular Organization of Lipopolysaccharides and Sensitizes the Gram-negative Bacteria.

Lakshminarayanan R, Tan WX, Aung TT, Goh ET, Muruganantham N, Li J, Chang JY, Dikshit N, Saraswathi P, Lim RR, Kang TS, Balamuralidhar V, Sukumaran B, Verma CS, Sivaraman J, Chaurasia SS, Liu S, Beuerman RW.

Sci Rep. 2016 May 13;6:25905. doi: 10.1038/srep25905.

26.

Insight into membrane selectivity of linear and branched polyethylenimines and their potential as biocides for advanced wound dressings.

Fox SJ, Fazil MH, Dhand C, Venkatesh M, Goh ET, Harini S, Eugene C, Lim RR, Ramakrishna S, Chaurasia SS, Beuerman RW, Verma CS, Verma NK, Loh XJ, Lakshminarayanan R.

Acta Biomater. 2016 Jun;37:155-64. doi: 10.1016/j.actbio.2016.04.015. Epub 2016 Apr 11.

PMID:
27079762
27.

Long range recognition and selection in IDPs: the interactions of the C-terminus of p53.

Kannan S, Lane DP, Verma CS.

Sci Rep. 2016 Mar 31;6:23750. doi: 10.1038/srep23750.

28.

The p53-Mdm2 interaction and the E3 ligase activity of Mdm2/Mdm4 are conserved from lampreys to humans.

Coffill CR, Lee AP, Siau JW, Chee SM, Joseph TL, Tan YS, Madhumalar A, Tay BH, Brenner S, Verma CS, Ghadessy FJ, Venkatesh B, Lane DP.

Genes Dev. 2016 Feb 1;30(3):281-92. doi: 10.1101/gad.274118.115. Epub 2016 Jan 21.

29.

Recognition Dynamics of p53 and MDM2: Implications for Peptide Design.

ElSawy KM, Lane DP, Verma CS, Caves LS.

J Phys Chem B. 2016 Jan 21;120(2):320-8. doi: 10.1021/acs.jpcb.5b11162. Epub 2016 Jan 11.

PMID:
26701330
30.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

Pradhan MR, Pal A, Hu Z, Kannan S, Chee Keong K, Lane DP, Verma CS.

Proteins. 2016 Feb;84(2):254-66. doi: 10.1002/prot.24976. Epub 2016 Jan 7.

PMID:
26677132
31.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

Tan YS, Spring DR, Abell C, Verma CS.

J Chem Theory Comput. 2015 Jul 14;11(7):3199-210. doi: 10.1021/ct5010577. Epub 2015 Jun 22.

PMID:
26575757
32.

R248Q mutation--Beyond p53-DNA binding.

Ng JW, Lama D, Lukman S, Lane DP, Verma CS, Sim AY.

Proteins. 2015 Dec;83(12):2240-50. doi: 10.1002/prot.24940. Epub 2015 Oct 27.

PMID:
26442703
33.

Gating by tryptophan 73 exposes a cryptic pocket at the protein-binding interface of the oncogenic eIF4E protein.

Lama D, Brown CJ, Lane DP, Verma CS.

Biochemistry. 2015 Oct 27;54(42):6535-44. doi: 10.1021/acs.biochem.5b00812. Epub 2015 Oct 9.

PMID:
26427906
34.

A search for synergy in the binding kinetics of Trastuzumab and Pertuzumab whole and F(ab) to Her2.

Lua WH, Gan SK, Lane DP, Verma CS.

NPJ Breast Cancer. 2015 Aug 5;1:15012. doi: 10.1038/npjbcancer.2015.12. eCollection 2015.

35.

A spatiotemporal characterization of the effect of p53 phosphorylation on its interaction with MDM2.

ElSawy KM, Sim A, Lane DP, Verma CS, Caves LS.

Cell Cycle. 2015;14(2):179-88. doi: 10.4161/15384101.2014.989043.

36.

Probing the binding mechanism of Mnk inhibitors by docking and molecular dynamics simulations.

Kannan S, Poulsen A, Yang HY, Ho M, Ang SH, Eldwin TS, Jeyaraj DA, Chennamaneni LR, Liu B, Hill J, Verma CS, Nacro K.

Biochemistry. 2015 Jan 13;54(1):32-46. doi: 10.1021/bi501261j. Epub 2014 Dec 5. Erratum in: Biochemistry. 2017 Nov 7;56(44):5964-5965.

PMID:
25431995
37.

mAb806 binding to epidermal growth factor receptor: a computational study.

Ng YZ, Kannan S, Lane DP, Fuentes G, Verma CS.

Proteins. 2015 Jan;83(1):153-68. doi: 10.1002/prot.24714. Epub 2014 Nov 18.

PMID:
25370927
38.

DNAApp: a mobile application for sequencing data analysis.

Nguyen PV, Verma CS, Gan SK.

Bioinformatics. 2014 Nov 15;30(22):3270-1. doi: 10.1093/bioinformatics/btu525. Epub 2014 Aug 5.

39.

Drugging the p53 pathway: understanding the route to clinical efficacy.

Khoo KH, Verma CS, Lane DP.

Nat Rev Drug Discov. 2014 Mar;13(3):217-36. doi: 10.1038/nrd4236. Review. Erratum in: Nat Rev Drug Discov. 2014 Apr;13(4):314. Hoe, Khoo Kian [corrected to Khoo, Kian Hoe].

PMID:
24577402
40.

Synthetic multivalent antifungal peptides effective against fungi.

Lakshminarayanan R, Liu S, Li J, Nandhakumar M, Aung TT, Goh E, Chang JY, Saraswathi P, Tang C, Safie SR, Lin LY, Riezman H, Lei Z, Verma CS, Beuerman RW.

PLoS One. 2014 Feb 3;9(2):e87730. doi: 10.1371/journal.pone.0087730. eCollection 2014.

41.

Exploiting protein intrinsic flexibility in drug design.

Lukman S, Verma CS, Fuentes G.

Adv Exp Med Biol. 2014;805:245-69. doi: 10.1007/978-3-319-02970-2_11. Review.

PMID:
24446365
42.

Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces.

Lama D, Quah ST, Verma CS, Lakshminarayanan R, Beuerman RW, Lane DP, Brown CJ.

Sci Rep. 2013 Dec 13;3:3451. doi: 10.1038/srep03451.

43.

Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

Lukman S, Lane DP, Verma CS.

PLoS One. 2013 Nov 12;8(11):e80221. doi: 10.1371/journal.pone.0080221. eCollection 2013.

44.

On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein.

ElSawy KM, Verma CS, Lane DP, Caves LS.

Cell Cycle. 2013 Dec 15;12(24):3727-35. doi: 10.4161/cc.27273. Epub 2013 Nov 21.

45.

A comparison and optimization of methods and factors affecting the transformation of Escherichia coli.

Chan WT, Verma CS, Lane DP, Gan SK.

Biosci Rep. 2013 Dec 12;33(6). pii: e00086. doi: 10.1042/BSR20130098.

46.

Differences in the binding affinities of ErbB family: heterogeneity in the prediction of resistance mutants.

Pereira M, Verma CS, Fuentes G.

PLoS One. 2013 Oct 23;8(10):e77054. doi: 10.1371/journal.pone.0077054. eCollection 2013.

47.

Dynamics of Bcl-xL in water and membrane: molecular simulations.

Maity A, Yadav S, Verma CS, Ghosh Dastidar S.

PLoS One. 2013 Oct 8;8(10):e76837. doi: 10.1371/journal.pone.0076837. eCollection 2013.

48.

Effect of Ser392 phosphorylation on the structure and dynamics of the polybasic domain of ADP ribosylation factor nucleotide site opener protein: a molecular simulation study.

Srinivasaraghavan K, Nacro K, Grüber G, Verma CS.

Biochemistry. 2013 Oct 15;52(41):7339-49. doi: 10.1021/bi400912e. Epub 2013 Oct 1.

PMID:
24083777
49.

On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study.

ElSawy KM, Verma CS, Joseph TL, Lane DP, Twarock R, Caves LS.

Cell Cycle. 2013 Feb 1;12(3):394-404. doi: 10.4161/cc.23511. Epub 2013 Jan 16.

50.

Stapled peptides with improved potency and specificity that activate p53.

Brown CJ, Quah ST, Jong J, Goh AM, Chiam PC, Khoo KH, Choong ML, Lee MA, Yurlova L, Zolghadr K, Joseph TL, Verma CS, Lane DP.

ACS Chem Biol. 2013 Mar 15;8(3):506-12. doi: 10.1021/cb3005148. Epub 2012 Dec 18.

PMID:
23214419

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