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We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two… (More)
The interconnected nature of interactions in protein structures appears to be the major hurdle in preventing the construction of accurate comparative models. We present an algorithm that uses graph theory to handle this problem. Each possible conformation of a residue in an amino acid sequence is represented using the notion of a node in a graph. Each node… (More)
A discriminatory function based on a statistical analysis of atomic contacts in protein structures is used for selecting side chain rotamers given a peptide main chain. The function allows us to rank different possible side chain conformations on the basis of contacts between side chain atoms and atoms in the environment. We compare the differences in… (More)
We constructed five comparative models in a blind manner for the second meeting on the Critical Assessment of protein Structure Prediction methods (CASP2). The method used is based on a novel graph-theoretic clique-finding approach, and attempts to address the problem of interconnected structural changes in the comparative modeling of protein structures. We… (More)
Comparative models of three proteins have been built using a variety of computational methods, heavily supplemented by visual inspection. We consider the accuracy obtained to be worse than expected. A careful analysis of the models shows that a major reason for the poor results is the interconnectedness of the structural differences between the target… (More)
In glassy isopentane at 77 K, 1-phenyl-4-(4-pyridyl)-cis-1,cis-3-butadiene (cc-PPyB) and 1-phenyl-4-(4-pyridyl)-cis-1,trans-3-butadiene (ct-PPyB) can undergo simultaneous two-bond photoisomerization. Under the same conditions, 1-phenyl-4-(4-pyridyl)-trans-1,cis-3-butadiene (tc-PPyB) gives tt-PPyB, the ultimate photoproduct in all cases.