The low level scoring matrices

• ijRkl should be based on superposition bond on ai and bj
• Define local reference systems around ai and bj e.g. by using (the Cas of) ai-1, ai, ai+1 and bj-1, bj, bj+1
• The coordinates of A’s and B’s residues are transformed into the respective coordinate systems
  
• One simple scoring scheme for aligning ak and bl depends only on the distance between ak and bl in their respective coordinate systems

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