Ariel Fernandez – Selected Publications

Selected publications of Ariel Fernández Ariel Fernandez Bibliography: 430 publications total. Ariel Fernández, Tobin R. Sosnick and Andrés Colubri: “Dynamics of hydrogen-bond desolvation in folding proteins”, Journal of Molecular Biology 321, 659-675 (2002). Ariel Fernández and Harold A. Scheraga: “Insufficiently dehydrated hydrogen bonds as determinants for protein interactions”, Proceedings of the National Academy of Sciences, […]

Ariel Fernandez May Have Created a WaterMap Precursor in 2007

Contributed by Weishi L. Meng, reproduced from Science Transparency.    Drug designers often implement molecular therapies to block malfunctioning proteins that are causing disease. They do so by creating small molecules that bind to the intended protein target when suitably delivered. The procedure has its risks as unintended targets (off-target proteins) may also be hit or […]

Physics at the Biomolecular Interface: Review on Ariel Fernandez’s Book by Weishi Meng

Book Review by Weishi Meng (Reproduced with permission) “Physics at the Biomolecular Interface” is the latest book by Ariel Fernandez (阿列尔·费尔南德斯), the physical chemist and mathematician who developed the center manifold thermodynamics, unraveling the physical basis for the onset of life, and discovered the dehydron (脱水元), an idea that laid the foundation for the new field of epistructural biology. The hardcover is […]

Rewriting the Mechanisms of Biological Chemistry: Dehydrons as Chemical Species

If you peruse any of the increasingly bulkier biochemistry textbooks you will notice that a large portion of the reactions depicted correspond mechanistically to transesterifications. Typically in these reactions, nucleophilic attacks are responsible for the breaking and forming of bonds at the catalytic site of the enzyme/substrate transient complex. Yet, something does not look quite […]

Structure-based drug discovery without structure: Working around the paradox to cure heart failure

Transcript on presentation by Ariel Fernandez for Drug Discovery Today (doi:10.1016/j.drudis.2015.10.006) Drug discovery has been focusing for some time on protein-protein (PP) associations, the basic molecular events in biology. The recruitment of protein complexes is required to initiate and propagate signaling cascades, regulate enzyme activity, articulate and control mechanistic processes involving molecular motors, etc. When […]

On “Promoting an Open Research Culture” (Science Magazine)

On 26 June 2015, Science magazine published an article in its section “Policy Forum” entitled “Promoting an Open Research Culture”  (B. A. Nosek et al. Science, Vol. 348, pp. 1422-1425, DOI: 10.1126/science.aab2374). The article and two related pieces (“Self-correction in science at work”, and “Solving reproducibility“) published in the same issue seem to have been inspired by the perception that there […]

New treatment for heart failure: US Patent 9,051,387 by Richard Moss and Ariel Fernandez

The recently awarded US patent number 9051387 describes the first therapeutic disruption of a protein-protein association using a rationally designed man-made ligand, a challenge considered the holy grail in drug discovery. This invention by Richard Moss and Ariel Fernandez provides basically a treatment of heart failure. At the molecular level, the effect of the drug is […]