José Ramón López-Blanco

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MOTIVATION Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on(More)
MOTIVATION Prediction of protein-protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of(More)
Keywords: Computational biology Macromolecular machines Normal modes Eigenvalue problems Krylov-subspace method Clusters of multicore processors a b s t r a c t Normal modes in internal coordinates (IC) furnish an excellent way to model functional collective motions of macromolecular machines, but exhibit a high computational cost when applied to(More)
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation(More)
Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service ( for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to(More)
UNLABELLED The prediction of protein-protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein-protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential.(More)
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