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Sidechain prediction is an important subproblem of protein design and structure prediction. Construction of rotamer library is the basis for protein sidechain prediction because it provides the basic searching space for prediction. However, the state-of-the-art rotamer libraries focus on the statistical information of individual amino acids, ignoring the direct affection of its adjacent amino acids...
Pyrophosphate-dependent phosphofructokinase (PPi-PFK) is the rate-limiting glycolytic enzyme found in the pathogenic protistsEntamoeba histolytica, Giardia lamblia, Toxoplasma gondii, Trichomonas vaginalis,andNaegleria fowleri.The enzyme differs significantly from ATP-dependent phosphofructokinases found in humans and as such represents an important drug target. Current therapy for infections caused...
Modeling by homology is the most accurate computational method for translating an amino acid sequence into a protein structure. Homology modeling can be divided into two sub-problems, placing the polypeptide backbone and adding side-chains. We present a method for rapidly predicting the conformations of protein side-chains, starting from main-chain coordinates alone. The method involves using fewer...
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