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We propose an improved prediction method of the tertiary structures of $alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because transmembrane helices of native membrane proteins are often distorted. In order to test the effectiveness of the present method, we applied it to the structure predictions of glycophorin A and phospholamban. The results were in accord with experiments.
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts MP contacts
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global conformational spa
Computational prediction of membrane protein (MP) structures is very challenging partially due to lack of sufficient solved structures for homology modeling. Recently direct evolutionary coupling analysis (DCA) sheds some light on protein contact pre
Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of proteins, for example, using the self-linking
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knots ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they diffuse arou