Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule

J Mol Biol. 1992 May 20;225(2):487-94. doi: 10.1016/0022-2836(92)90934-c.


A new strategy for predicting the topology of bacterial inner membrane proteins is proposed on the basis of hydrophobicity analysis, automatic generation of a set of possible topologies and ranking of these according to the positive-inside rule. A straightforward implementation with no attempts at optimization predicts the correct topology for 23 out of 24 inner membrane proteins with experimentally determined topologies, and correctly identifies 135 transmembrane segments with only one overprediction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Hydrogen-Ion Concentration
  • Membrane Proteins / chemistry*
  • Protein Conformation*
  • Water


  • Bacterial Proteins
  • Membrane Proteins
  • Water