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Your search keyword '"José Ignacio Garzón"' showing total 2 results
Start Over Author "José Ignacio Garzón" Journal bioinformatics (oxford, england)
2 results on '"José Ignacio Garzón"'

1. DFprot: a webtool for predicting local chain deformability

Author

José Ignacio Garzón, Pablo Chacón, Ruben Abagyan, and Julio A. Kovacs

Subjects
Statistics and Probability, Models, Molecular, Computer science, Interface (Java), Protein Conformation, Molecular Sequence Data, Bioinformatics, Biochemistry, Computational science, Upload, Protein structure, Chain (algebraic topology), Sequence Analysis, Protein, Computer Simulation, Amino Acid Sequence, Molecular Biology, Flexibility (engineering), Internet, Proteins, Elasticity, Computer Science Applications, Protein Structure, Tertiary, Computational Mathematics, Computational Theory and Mathematics, Models, Chemical, Sequence Alignment, Algorithms, Software
Abstract

Summary: DFprot is a web-based server for predicting main-chain deformability from a single protein conformation. The server automatically performs a normal-mode analysis (NMA) of the uploaded structure and calculates its capability to deform at each of its residues. Non-specialists can easily and rapidly obtain a quantitative first approximation of the flexibility of their structures with a simple and efficient interface. Availability: http://sbg.cib.csic.es/Software/DFprot Contact: pablo@cib.csic.es

Published
2007

2. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

Author

José Ignacio Garzón, Ruben Abagyan, Julio A. Kovacs, and Pablo Chacón

Subjects
Statistics and Probability, Models, Molecular, Binding Sites, Computer science, Protein Conformation, Protein domain, Spherical harmonics, Proteins, Reproducibility of Results, Biochemistry, Sensitivity and Specificity, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Models, Chemical, Multi resolution, Docking (molecular), Sequence Analysis, Protein, DOCK, Protein Interaction Mapping, Computer Simulation, Molecular Biology, Algorithm, Algorithms, Protein Binding
Abstract

Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. Results: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. Availability: Contact: pablo@cib.csic.es Supplementary information: Supplementary data are available at Bioinformatics online.

Published
2006

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