Computational Drug Discovery and Design

(backadmin) #1
computing structural and physicochemical fea-
tures of proteins and peptides from amino acid
sequence. Nucleic Acids Res 39:W385–W390


  1. Du P, Wang X, Xu C, Gao Y (2012) PseAAC-
    builder: a cross-platform stand-alone program
    for generating various special Chou’s pseudo-
    amino acid compositions. Anal Biochem
    425:117–119

  2. Shen HB, Chou KC (2008) PseAAC: a flexible
    web server for generating various kinds of pro-
    tein pseudo amino acid composition. Anal Bio-
    chem 373:386–388

  3. Chou KC (2001) Prediction of protein cellular
    attributes using pseudo-amino acid composi-
    tion. Proteins 43:246–255

  4. Liu B, Liu F, Wang X, Chen J, Fang L, Chou
    KC (2015) Pse-in-one: a web server for gener-
    ating various modes of pseudo components of
    DNA, RNA, and protein sequences. Nucleic
    Acids Res 43:W65–W71

  5. Ruiz-Blanco YB, Paz W, Green J, Marrero-
    Ponce Y (2015) ProtDCal: a program to com-
    pute general-purpose-numerical descriptors for
    sequences and 3D-structures of proteins. BMC
    Bioinformatics 16:162

  6. Cao DS, Xu QS, Liang YZ (2013) Propy: a tool
    to generate various modes of Chou’s PseAAC.
    Bioinformatics 29:960–962

  7. Xiao N, Cao DS, Zhu MF, Xu QS (2015)
    Protr/ProtrWeb: R package and web server
    for generating various numerical representa-
    tion schemes of protein sequences. Bioinfor-
    matics 31:1857–1859

  8. Yap CW (2011) PaDEL-descriptor: an open
    source software to calculate molecular descrip-
    tors and fingerprints. J Comput Chem
    32:1466–1474
    35. Li ZR, Han LY, Xue Y, Yap CW, Li H, Jiang L
    (2007) MODEL—molecular descriptor lab: a
    web-based server for computing structural and
    physicochemical features of compounds. Bio-
    technol Bioeng 97:389–396
    36. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L
    (2008) Mold2, molecular descriptors from 2D
    structures for Chemoinformatics and Toxicoin-
    formatics. J Chem Inf Comput Sci
    48:1337–1344
    37. Chawla NV, Bowyer KW, Hall LO, Kegelmeyer
    WP (2002) SMOTE: synthetic minority over-
    sampling technique. J Artif Intell Res
    16:321–357
    38. Witten IH, Frank E, Hall MA (eds) (2011)
    Data mining: practical machine learning tools
    and techniques. Morgan Kaufmann Publishers
    Inc., San Francisco
    39. Bradley AP (1997) The use of the area under
    the ROC curve in the evaluation of machine
    learning algorithms. Pattern Recogn
    30:1145–1159
    40. Szklarczyk D, Franceschini A, Wyder S,
    Forslund K, Heller D, Huerta-Cepas J et al
    (2015) STRING v10: protein–protein interac-
    tion networks, integrated over the tree of life.
    Nucleic Acids Res 43:D447–D452
    41. Chatr-aryamontri A, Oughtred R, Boucher L,
    Rust J, Chang C, Kolas NK et al (2017) The
    BioGRID interaction database: 2017 update.
    Nucleic Acids Res 45:D369–D379
    42. Keshava Prasad TS, Goel R, Kandasamy K,
    Keerthikumar S, Kumar S, Mathivanan S et al
    (2009) Human protein reference database--
    2009 update. Nucleic Acids Res 37:
    D767–D772


30 Abhigyan Nath et al.

Free download pdf