R/instaindex.R

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

#' @export instaIndex
#' @title Compute the instability index of a protein sequence
#' @description This function calculates the instability index proposed by Guruprasad (1990). This index predicts the stability of a protein based on its amino acid composition, a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.
#' @param seq An amino-acids sequence
#' @return The computed instability index for a given amino-acids sequence
#' @references Guruprasad K, Reddy BV, Pandit MW (1990). "Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence". Protein Eng. 4 (2): 155 - 61. doi:10.1093/protein/4.2.155
#' @examples
#' # COMPARED TO ExPASy INSTAINDEX
#' # http://web.expasy.org/protparam/
#' # SEQUENCE: QWGRRCCGWGPGRRYCVRWC
#' # The instability index (II) is computed to be 83.68
#'
#' instaIndex(seq = "QWGRRCCGWGPGRRYCVRWC")
#' # [1] 83.68
#'
instaIndex <- function(seq) {
  # Setting the Guruprasad scale
  guruprasad <-
    c(
      WW = 1,
      WC = 1,
      WM = 24.68,
      WH = 24.68,
      WY = 1,
      WF = 1,
      WQ = 1,
      WN = 13.34,
      WI = 1,
      WR = 1,
      WD = 1,
      WP = 1,
      WT = -14.03,
      WK = 1,
      WE = 1,
      WV = -7.49,
      WS = 1,
      WG = -9.37,
      WA = -14.03,
      WL = 13.34,
      CW = 24.68,
      CC = 1,
      CM = 33.6,
      CH = 33.6,
      CY = 1,
      CF = 1,
      CQ = -6.54,
      CN = 1,
      CI = 1,
      CR = 1,
      CD = 20.26,
      CP = 20.26,
      CT = 33.6,
      CK = 1,
      CE = 1,
      CV = -6.54,
      CS = 1,
      CG = 1,
      CA = 1,
      CL = 20.26,
      MW = 1,
      MC = 1,
      MM = -1.88,
      MH = 58.28,
      MY = 24.68,
      MF = 1,
      MQ = -6.54,
      MN = 1,
      MI = 1,
      MR = -6.54,
      MD = 1,
      MP = 44.94,
      MT = -1.88,
      MK = 1,
      ME = 1,
      MV = 1,
      MS = 44.94,
      MG = 1,
      MA = 13.34,
      ML = 1,
      HW = -1.88,
      HC = 1,
      HM = 1,
      HH = 1,
      HY = 44.94,
      HF = -9.37,
      HQ = 1,
      HN = 24.68,
      HI = 44.94,
      HR = 1,
      HD = 1,
      HP = -1.88,
      HT = -6.54,
      HK = 24.68,
      HE = 1,
      HV = 1,
      HS = 1,
      HG = -9.37,
      HA = 1,
      HL = 1,
      YW = -9.37,
      YC = 1,
      YM = 44.94,
      YH = 13.34,
      YY = 13.34,
      YF = 1,
      YQ = 1,
      YN = 1,
      YI = 1,
      YR = -15.91,
      YD = 24.68,
      YP = 13.34,
      YT = -7.49,
      YK = 1,
      YE = -6.54,
      YV = 1,
      YS = 1,
      YG = -7.49,
      YA = 24.68,
      YL = 1,
      FW = 1,
      FC = 1,
      FM = 1,
      FH = 1,
      FY = 33.6,
      FF = 1,
      FQ = 1,
      FN = 1,
      FI = 1,
      FR = 1,
      FD = 13.34,
      FP = 20.26,
      FT = 1,
      FK = -14.03,
      FE = 1,
      FV = 1,
      FS = 1,
      FG = 1,
      FA = 1,
      FL = 1,
      QW = 1,
      QC = -6.54,
      QM = 1,
      QH = 1,
      QY = -6.54,
      QF = -6.54,
      QQ = 20.26,
      QN = 1,
      QI = 1,
      QR = 1,
      QD = 20.26,
      QP = 20.26,
      QT = 1,
      QK = 1,
      QE = 20.26,
      QV = -6.54,
      QS = 44.94,
      QG = 1,
      QA = 1,
      QL = 1,
      NW = -9.37,
      NC = -1.88,
      NM = 1,
      NH = 1,
      NY = 1,
      NF = -14.03,
      NQ = -6.54,
      NN = 1,
      NI = 44.94,
      NR = 1,
      ND = 1,
      NP = -1.88,
      NT = -7.49,
      NK = 24.68,
      NE = 1,
      NV = 1,
      NS = 1,
      NG = -14.03,
      NL = 1,
      IW = 1,
      IC = 1,
      IM = 1,
      IH = 13.34,
      IY = 1,
      IF = 1,
      IQ = 1,
      IN = 1,
      II = 1,
      IR = 1,
      ID = 1,
      IP = -1.88,
      IT = 1,
      IK = -7.49,
      IE = 44.94,
      IV = -7.49,
      IS = 1,
      IG = 1,
      IA = 1,
      IL = 20.26,
      RW = 58.28,
      RC = 1,
      RM = 1,
      RH = 20.26,
      RY = -6.54,
      RF = 1,
      RQ = 20.26,
      RN = 13.34,
      RI = 1,
      RR = 58.28,
      RD = 1,
      RP = 20.26,
      RT = 1,
      RK = 1,
      RE = 1,
      RV = 1,
      RS = 44.94,
      RG = -7.49,
      RA = 1,
      RL = 1,
      DW = 1,
      DC = 1,
      DM = 1,
      DH = 1,
      DY = 1,
      DF = -6.54,
      DQ = 1,
      DN = 1,
      DI = 1,
      DR = -6.54,
      DD = 1,
      DP = 1,
      DT = -14.03,
      DK = -7.49,
      DE = 1,
      DV = 1,
      DS = 20.26,
      DG = 1,
      DA = 1,
      DL = 1,
      PW = -1.88,
      PC = -6.54,
      PM = -6.54,
      PH = 1,
      PY = 1,
      PF = 20.26,
      PQ = 20.26,
      PN = 1,
      PI = 1,
      PR = -6.54,
      PD = -6.54,
      PP = 20.26,
      PT = 1,
      PK = 1,
      PE = 18.38,
      PV = 20.26,
      PS = 20.26,
      PG = 1,
      PA = 20.26,
      PL = 1,
      TW = -14.03,
      TC = 1,
      TM = 1,
      TH = 1,
      TY = 1,
      TF = 13.34,
      TQ = -6.54,
      TN = -14.03,
      TI = 1,
      TR = 1,
      TD = 1,
      TP = 1,
      TT = 1,
      TK = 1,
      TE = 20.26,
      TV = 1,
      TS = 1,
      TG = -7.49,
      TA = 1,
      TL = 1,
      KW = 1,
      KC = 1,
      KM = 33.6,
      KH = 1,
      KY = 1,
      KF = 1,
      KQ = 24.68,
      KN = 1,
      KI = -7.49,
      KR = 33.6,
      KD = 1,
      KP = -6.54,
      KT = 1,
      KK = 1,
      KE = 1,
      KV = -7.49,
      KS = 1,
      KG = -7.49,
      KA = 1,
      KL = -7.49,
      EW = -14.03,
      EC = 44.94,
      EM = 1,
      EH = -6.54,
      EY = 1,
      EF = 1,
      EQ = 20.26,
      EN = 1,
      EI = 20.26,
      ER = 1,
      ED = 20.26,
      EP = 20.26,
      ET = 1,
      EK = 1,
      EE = 33.6,
      EV = 1,
      ES = 20.26,
      EG = 1,
      EA = 1,
      EL = 1,
      VW = 1,
      VC = 1,
      VM = 1,
      VH = 1,
      VY = -6.54,
      VF = 1,
      VQ = 1,
      VN = 1,
      VI = 1,
      VR = 1,
      VD = -14.03,
      VP = 20.26,
      VT = -7.49,
      VK = -1.88,
      VE = 1,
      VV = 1,
      VS = 1,
      VG = -7.49,
      VA = 1,
      VL = 1,
      SW = 1,
      SC = 33.6,
      SM = 1,
      SH = 1,
      SY = 1,
      SF = 1,
      SQ = 20.26,
      SN = 1,
      SI = 1,
      SR = 20.26,
      SD = 1,
      SP = 44.94,
      ST = 1,
      SK = 1,
      SE = 20.26,
      SV = 1,
      SS = 20.26,
      SG = 1,
      SA = 1,
      SL = 1,
      GW = 13.34,
      GC = 1,
      GM = 1,
      GH = 1,
      GY = -7.49,
      GF = 1,
      GQ = 1,
      GN = -7.49,
      GI = -7.49,
      GR = 1,
      GD = 1,
      GP = 1,
      GT = -7.49,
      GK = -7.49,
      GE = -6.54,
      GV = 1,
      GS = 1,
      GG = 13.34,
      GA = -7.49,
      GL = 1,
      AW = 1,
      AC = 44.94,
      AM = 1,
      AH = -7.49,
      AY = 1,
      AF = 1,
      AQ = 1,
      AN = 1,
      AI = 1,
      AR = 1,
      AD = -7.49,
      AP = 20.26,
      AT = 1,
      AK = 1,
      AE = 1,
      AV = 1,
      AS = 1,
      AG = 1,
      AA = 1,
      AL = 1,
      LW = 24.68,
      LC = 1,
      LM = 1,
      LH = 1,
      LY = 1,
      LF = 1,
      LQ = 33.6,
      LN = 1,
      LI = 1,
      LR = 20.26,
      LD = 1,
      LP = 20.26,
      LT = 1,
      LK = -7.49,
      LE = 1,
      LV = 1,
      LS = 1,
      LG = 1,
      LA = 1,
      LL = 1,
      'NA' = 1
    )
  # Divide the amino acid sequence in dipeptides
  aa <- aaCheck(seq)
  dp <- lapply(aa, function(aa) {
    apply(embed(aa, 2)[, 2:1], 1, paste0, collapse = "")
  })
  # Apply the formula:
  # (10/L)*sum(DIWV(XiYi+1) for each dipeptide)
  # Return the index value rounded to 2 decimals
  gp <- lapply(dp, function(dp) {
    (10 / (length(dp) + 1)) * sum(guruprasad[dp], na.rm = TRUE)
  })
  return(unlist(gp))
}