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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)

- Juliano B Francisco, José Mario Martínez, Leandro Martínez
- 2005

A theory of globally convergent trust-region methods for self-consistent field electronic structure calculations that use the density matrices as variables is developed. The optimization is performed by means of sequential global minimizations of a quadratic model of the true energy. The global minimization of this quadratic model, subject to the… (More)

- Élodie Laine, Leandro Martínez, Daniel Ladant, Thérèse Malliavin, Arnaud Blondel
- Toxins
- 2012

Edema Factor (EF) is a component of Bacillus anthracis toxin essential for virulence. Its adenylyl cyclase activity is induced by complexation with the ubiquitous eukaryotic cellular protein, calmodulin (CaM). EF and its complexes with CaM, nucleotides and/or ions, have been extensively characterized by X-ray crystallography. Those structural data allowed… (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)

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)

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)

Large-scale electronic structure calculations usually involve huge nonlinear eigenvalue problems. A method for solving these problems without employing expensive eigenvalue decompositions of the Fock matrix is presented in this work. The sparsity of the input and output matrices is preserved at every iteration, and the memory required by the algorithm… (More)

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)