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10.1002/prot.1145.abs The design of scoring functions (or potentials) for threading, differentiating native‐like from non‐native structures with a limited computational cost, is an active field of research. We revisit two widely used families of threading potentials: the pairwise and profile...
10.1002/prot.1137.abs HIV‐1 reverse transcriptase (RT) is one of the main targets for drugs used in the treatment of AIDS, among them, the non‐nucleoside RT inhibitors (NNRTIs). The flexibility of RT unliganded and complexed to double‐stranded DNA (RT/dsDNA), in water, has been studied by...
10.1002/prot.1144.abs The lipoamide arm of the H protein plays a pivotal role in the catalytic cycle of the glycine decarboxylase complex (GDC) by being successively methylamine loaded (Hmet), reduced (Hred), and oxidized (Hox). In a previous study, we calculated free‐energy surfaces as a...
10.1002/prot.1143.abs The concentration of melanin determines the intensity of colors of the skin and hair of animals. Melanin pigments are tyrosine‐based polymers formed in melanocytes within specialized organelles called melanosomes. In order to understand the mechanism of melanin...
10.1002/prot.1138.abs I report herein two 2.0 ns (1.0 fs time step) MD simulations of two zinc complexes bridged by a hydroxide in phosphotriesterase (PTE) employing the nonbonded method and the cationic dummy atom method that uses virtual atoms to impose orientational requirement for zinc...
10.1002/prot.1136.abs To date, a number of p53‐derived peptides have been evaluated in vitro for their ability to inhibit the carcinogenic p53–mdm2 interaction. Design of second‐generation nonpeptidic compounds requires the reduction of large peptide structures down to small molecules...
10.1002/prot.1146.abs Several protein sequence analysis algorithms are based on properties of amino acid composition and repetitiveness. These include methods for prediction of secondary structure elements, coiled‐coils, transmembrane segments or signal peptides, and for assignment of...
10.1002/prot.1139.abs Association of a protein complex follows a two‐step mechanism, with the first step being the formation of an encounter complex that evolves into the final complex. Here, we analyze recent experimental data of the association of TEM1‐β‐lactamase with BLIP using...
10.1002/prot.1142.abs We present here three high‐resolution crystal structures of complexes between the DNA‐binding domain of the heat‐shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat‐shock element, the...
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