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SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments
Author(s) -
Audic Stéphane,
Lopez Fabrice,
Claverie JeanMichel,
Poirot Olivier,
Abergel Chantal
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199710)29:2<252::aid-prot12>3.0.co;2-n
Subject(s) - java applet , software , computer science , simulated annealing , a priori and a posteriori , backtracking , java , pairwise comparison , set (abstract data type) , crystallization , programming language , algorithm , artificial intelligence , chemical engineering , engineering , philosophy , epistemology
SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr.