Julio A Kovacs
Affiliation: The Scripps Research Institute
- Fast rotational matchingJulio A Kovacs
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Acta Crystallogr D Biol Crystallogr 58:1282-6. 2002..Applications to the docking of atomic structures into electron-microscopy maps and the molecular-replacement problem in X-ray crystallography are considered...
- Predictions of protein flexibility: first-order measuresJulio A Kovacs
Department of Molecular Biology, The Scripps Research Institute La Jolla, California 92037, USA
Proteins 56:661-8. 2004..Deformability calculations correlate well with experimental results and validate the applicability of this method to protein flexibility predictions...
- Computational prediction of atomic structures of helical membrane proteins aided by EM mapsJulio A Kovacs
Department of Molecular Biology, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
Biophys J 93:1950-9. 2007..In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL...
- Damped-dynamics flexible fittingJulio A Kovacs
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
Biophys J 95:3192-207. 2008..Applications to the computation of transition pathways between known conformers, homology and loop modeling, as well as protein docking, are also discussed...
- Molecular modeling and mutagenesis of gap junction channelsJulio A Kovacs
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Prog Biophys Mol Biol 94:15-28. 2007..In spite of this substantial progress in understanding the structural biology of gap junction channels, an experimentally determined structure at atomic resolution will be essential to confirm these concepts...
- 2D fast rotational matching for image processing of biophysical dataYao Cong
School of Health Information Sciences and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 7000 Fannin St, Suite 600, Houston, TX 77030, USA
J Struct Biol 144:51-60. 2003..FRM2D exhibits a comparable or higher robustness against noise and a significant gain in efficiency that depends on the fineness of the angular sampling and linear search range...