Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices.
Nicola CannataStefano ToppoChiara RomualdiGiorgio VallePublished in: Bioinform. (2002)
Keyphrases
- amino acids
- branch and bound algorithm
- lower bound
- branch and bound
- protein sequences
- upper bound
- np hard
- combinatorial optimization
- sequence alignment
- secondary structure
- lower bounding
- precedence constraints
- randomly generated problems
- optimal solution
- single machine scheduling problem
- protein function
- upper bounding
- amino acid sequences
- protein structure prediction
- search algorithm
- lagrangian relaxation
- protein folding
- protein structure
- mixed integer linear programming
- search space
- contact map
- finding an optimal solution
- physico chemical
- max sat
- computational biology
- traveling salesman problem
- scheduling problem
- maximum clique
- pairwise