User profiles for Ahmet Bakan
Ahmet BakanSoftware Engineer at Google Verified email at google.com Cited by 3388 |
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths and …
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths and …
In vitro platforms for evaluating liver toxicity
The liver is a heterogeneous organ with many vital functions, including metabolism of
pharmaceutical drugs and is highly susceptible to injury from these substances. The etiology of …
pharmaceutical drugs and is highly susceptible to injury from these substances. The etiology of …
Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
Modeling protein flexibility constitutes a major challenge in accurate prediction of protein–ligand
and protein–protein interactions in docking simulations. The lack of a reliable method …
and protein–protein interactions in docking simulations. The lack of a reliable method …
ProDy: Protein Dynamics Inferred from Theory and Experiments
We developed a Python package, ProDy, for structure-based analysis of protein dynamics.
ProDy allows for quantitative characterization of structural variations in heterogeneous …
ProDy allows for quantitative characterization of structural variations in heterogeneous …
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
The conformational flexibility of target proteins continues to be a major challenge in accurate
modeling of protein–inhibitor interactions. A fundamental issue, yet to be clarified, is …
modeling of protein–inhibitor interactions. A fundamental issue, yet to be clarified, is …
Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages
G Molina, A Vogt, A Bakan, W Dai… - Nature chemical …, 2009 - nature.com
The dual-specificity phosphatase 6 (Dusp6) functions as a feedback regulator of fibroblast
growth factor (FGF) signaling to limit the activity of extracellular signal–regulated kinases (…
growth factor (FGF) signaling to limit the activity of extracellular signal–regulated kinases (…
Evol and ProDy for bridging protein sequence evolution and structural dynamics
Correlations between sequence evolution and structural dynamics are of utmost importance
in understanding the molecular mechanisms of function and their evolution. We have …
in understanding the molecular mechanisms of function and their evolution. We have …
Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules
Druggability assessment of a target protein has emerged in recent years as an important
concept in hit-to-lead optimization. A reliable and physically relevant measure of druggability …
concept in hit-to-lead optimization. A reliable and physically relevant measure of druggability …
An improved ZCT-PWM DC-DC converter for high-power and frequency applications
In this paper, an improved active resonant snubber cell that overcomes most of the drawbacks
of the normal zero-current transition (ZCT) pulsewidth-modulation (PWM) dc-dc converter …
of the normal zero-current transition (ZCT) pulsewidth-modulation (PWM) dc-dc converter …
[HTML][HTML] Towards a three-dimensional microfluidic liver platform for predicting drug efficacy and toxicity in humans
Although the process of drug development requires efficacy and toxicity testing in animals
prior to human testing, animal models have limited ability to accurately predict human …
prior to human testing, animal models have limited ability to accurately predict human …