Computational Drug Discovery and Design

(backadmin) #1

  1. Suzuki Y (2017) Predicting receptor function-
    ality of signaling lymphocyte activation mole-
    cule for measles virus hemagglutinin from
    docking simulation. Microbiol Immunol.
    https://doi.org/10.1111/1348-0421.12484

  2. Dar HA, Zaheer T, Paracha RZ, Ali A (2017)
    Structural analysis and insight into Zika virus
    NS5 mediated interferon inhibition. Infect
    Genet Evol 51:143–152.https://doi.org/10.
    1016/j.meegid.2017.03.027

  3. Antal Z, Szoverfi J, Fejer SN (2017) Predicting
    the initial steps of salt-stable cowpea chlorotic
    mottle virus capsid assembly with atomistic
    force fields. J Chem Inf Model 57:910–917.
    https://doi.org/10.1021/acs.jcim.7b00078

  4. Hossain MS, Azad AK, Chowdhury PA,
    Wakayama M (2017) Computational identifi-
    cation and characterization of a promiscuous
    T-cell epitope on the extracellular protein 85B
    of mycobacterium spp. for peptide-based sub-
    unit vaccine design. Biomed Res Int
    2017:4826030. https://doi.org/10.1155/
    2017/4826030

  5. He Y, Xiang Z, Mobley HLT (2010) Vaxign:
    the first web-based vaccine design program for
    reverse vaccinology and applications for vaccine
    development. J Biomed Biotechnol
    2010:297505. https://doi.org/10.1155/
    2010/297505

  6. Totrov M, Abagyan R (1997) Flexible protein-
    ligand docking by global energy optimization
    in internal coordinates. Proteins (Suppl
    1):215–220

  7. Rawal L, Panwar D, Ali S (2017) Intermolecu-
    lar interactions between DMαand DMβpro-
    teins in BuLA-DM complex of water buffalo
    Bubalus bubalis. J Cell Biochem.https://doi.
    org/10.1002/jcb.26075

  8. Dundas J, Ouyang Z, Tseng J et al (2006)
    CASTp: computed atlas of surface topography
    of proteins with structural and topographical
    mapping of functionally annotated residues.
    Nucleic Acids Res 34:W116–W118.https://
    doi.org/10.1093/nar/gkl282

  9. Krissinel E, Henrick K (2007) Inference of
    macromolecular assemblies from crystalline
    state. J Mol Biol 372:774–797.https://doi.
    org/10.1016/j.jmb.2007.05.022

  10. Sinha VK, Sharma OP, Kumar MS (2017)
    Insight into the intermolecular recognition
    mechanism involved in complement compo-
    nent 4 activation through serine protease-
    trypsin. J Biomol Struct Dyn:1–15.https://
    doi.org/10.1080/07391102.2017.1288658

  11. Prakash P, Sayyed-Ahmad A, Cho KJ et al
    (2017) Computational and biochemical char-
    acterization of two partially overlapping


interfaces and multiple weak-affinity K-Ras
dimers. Sci Rep 7:40109.https://doi.org/10.
1038/srep40109


  1. Congreve M, Langmead CJ, Mason JS, Mar-
    shall FH (2011) Progress in structure based
    drug design for G protein-coupled receptors.
    J Med Chem 54:4283–4311.https://doi.org/
    10.1021/jm200371q

  2. Pierce KL, Premont RT, Lefkowitz RJ (2002)
    Seven-transmembrane receptors. Nat Rev Mol
    Cell Biol 3:639–650. https://doi.org/10.
    1038/nrm908

  3. Gilman AG (1987) G proteins: transducers of
    receptor-generated signals. Annu Rev Biochem
    56:615–649. https://doi.org/10.1146/
    annurev.biochem.56.1.615

  4. Bouvier M (2001) Oligomerization of G-
    protein-coupled transmitter receptors. Nat
    Rev Neurosci 2:274–286. https://doi.org/
    10.1038/35067575

  5. Ferre S, Casado V, Devi LA et al (2014) G
    protein-coupled receptor oligomerization
    revisited: functional and pharmacological per-
    spectives. Pharmacol Rev 66:413–434.
    https://doi.org/10.1124/pr.113.008052

  6. Gonza ́lez-Maeso J (2011) GPCR oligomers in
    pharmacology and signaling. Mol Brain 4:20.
    https://doi.org/10.1186/1756-6606-4-20

  7. Kniazeff J, Pre ́zeau L, Rondard P et al (2011)
    Dimers and beyond: the functional puzzles of
    class C GPCRs. Pharmacol Ther 130:9–25.
    https://doi.org/10.1016/j.pharmthera.2011.
    01.006

  8. Bellot M, Galandrin S, Boularan C et al (2015)
    Dual agonist occupancy of AT1-R-α2C-AR
    heterodimers results in atypical Gs-PKA signal-
    ing. Nat Chem Biol 11:271–279.https://doi.
    org/10.1038/nchembio.1766

  9. Rashid AJ, So CH, Kong MMC et al (2007)
    D1–D2 dopamine receptor heterooligomers
    with unique pharmacology are coupled to
    rapid activation of Gq/11 in the striatum.
    Proc Natl Acad Sci U S A 104:654–659.
    https://doi.org/10.1073/pnas.0604049104

  10. Han Y, Moreira IS, Urizar E et al (2009) Allo-
    steric communication between protomers of
    dopamine class A GPCR dimers modulates
    activation. Nat Chem Biol 5:688–695.
    https://doi.org/10.1038/nchembio.199

  11. Smith NJ, Milligan G (2010) Allostery at G
    protein-coupled receptor homo- and hetero-
    mers: uncharted pharmacological landscapes.
    Pharmacol Rev 62:701–725.https://doi.org/
    10.1124/pr.110.002667

  12. Bouvier M, He ́bert TE (2014) CrossTalk pro-
    posal: weighing the evidence for class A GPCR
    dimers, the evidence favours dimers. J Physiol


Protein-Protein Docking 303
Free download pdf