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Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances.… (More)

Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems. The theories and techniques developed for structural and thermodynamic analyses are well established, and many software packages are available. However, designing starting configurations for dynamics can be cumbersome. Easily… (More)

An inexact restoration (IR) approach is presented to solve a matricial optimization problem arising in electronic structure calculations. The solution of the problem is the closed-shell density matrix and the constraints are represented by a Grassmann manifold. One of the mathematical and computational challenges in this area is to develop methods for… (More)

BACKGROUND
Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural similarities. However, current practical methods are seldom supported by convergence theories. In particular, although the goal of each… (More)

Given r real functions F 1 (x),. .. , F r (x) and an integer p between 1 and r, the Low Order-Value Optimization problem (LOVO) consists of minimizing the sum of the functions that take the p smaller values. If (y 1 ,. .. , y r) is a vector of data and T (x, t i) is the predicted value of the observation i with the parameters x ∈ IR n , it is natural to… (More)

Structural Alignment is an important tool for fold identification of proteins, structural screening on ligand databases, pharmacophore identification and other applications. In the general case, the optimization problem of superimposing two structures is nonsmooth and noncon-vex, so that most popular methods are heuristic and do not employ derivative… (More)

- Marcelo Vizoná Liberato, Alessandro S. Nascimento, Steven D. Ayers, Jean Z. Lin, Aleksandra Cvoro, Rodrigo L. Silveira +13 others
- PloS one
- 2012

Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPARγ ligand binding domain (LBD) and found that the ligand… (More)

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic… (More)

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