Protein Interaction

BIGGER (BImolecular complex Generation with Global Evaluation and Ranking), developed by Ludwig Krippahl and Nuno Palma, is an algorithm for searching possible configurations of protein complexes and finding the most likely models for the interaction. It relies on constraint programming techniques for an efficient search and to use relevant data from any experimental technique that can provide information about the interaction.
The relevant publications on this work are:
         • Modeling Protein Complexes with BiGGER
          Krippahl L, Moura JJG, Palma PN
          Proteins (2003) 52:19-23
         • A New (Soft)Docking Algorithm for Predicting Protein Interactions
          Palma PN, Krippahl L, Wampler JW, Moura JJG
          Protein Struc Func Gen (2000) 39:372-84
Our most recent publications using the program to model protein-protein complexes involved in electron transfer chains are:
         • The electron transfer complex between nitrous oxide reductase and its electron donors
          Dell'Acqua S, Moura I, Moura JJ, Pauleta SR
          J Biol Inorg Chem (2011) 16:1241-1254
         • Rubredoxin as a paramagnetic relaxation-inducing probe
          Almeida RM, Pauleta SR, Moura I, Moura JJ
          J Inorg BIochem (2009) 103:1245-1253

Modelling and Computation

Chemera is an application that serves as interface for PSICO and BiGGER and also includes a set of tools to visualise and manipulate structures, integrate information from remote services and compute some electrostatic properties of proteins.

You can download Chemera and BiGGER from the Chemera page