Side-Chains with Rotamer Library SCWRL

Side-Chains with Rotamer Library (SCWRL) 

In addition to predicting the backbone conformation correctly, one also needs to predict the conformation of the attached amino acid residue side chains. The rotational conformations of these side chains are referred to as rotamers. The side-chain orientation of amino acid residues typically occupy one of several discrete conformations.The maximum number of possible rotamers for a protein is 

Number of Protein Structures = Number of Rotamers Residues  

The rotamer library used by SCWRL is backbone-dependent. Such libraries are considered to be more accurate than a backbone-independent rotamer library. A backbone-dependent rotamer library is more robust because the side-chain conformations are based on the protein s backbone dihedral angles ( l and Both the secondary structure and the 

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SCWRL uses an alternative strategy, based on a probabilistic potential based on the backbone-dependent rotamer library. There are two terms the internal side-chain energy and the local side-chain-backbone interaction are modeled with an energy term proportional to —In prot where prot is the probability of the rotamer for the particular side-chain type and backbone conformation and a simple truncated linear steric term that models the repulsive interactions between atoms [93, 94]. 

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