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The optimization of nonlinear functions using particle swarm methodology is described. Implementations of two paradigms are discussed and compared, including a recently developed locally oriented paradigm. Benchmark test...

A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented. For each element only one auxiliary basis set is needed to approximate Coulomb energies in conjunctio...

An analogy with the way ant colonies function has suggested the definition of a new computational paradigm, which we call ant system (AS). We propose it as a viable new approach to stochastic combinatorial optimization. ...

We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute sum...

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related are...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles. As knowledge of cancer mechanisms has p...

BACKGROUND: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reporte...

MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and ...

A method of ‘‘natural population analysis’’ has been developed to calculate atomic charges and orbital populations of molecular wave functions in general atomic orbital basis sets. The natural analysis is an alte...

A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calcu...

Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein-protein interactions are particularly important due to their versatility, specificity and adaptabi...

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the infor...

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assist...

Clustering task aims at the unsupervised classification of patterns (e.g., observations, data, vec- tors, etc.) in different groups. Clustering problem has been approached from different disciplines during the last years...

Three alternatives within the method of assignment by classes are presented for the calculation of individuals lifetime in genetic algorithms with varying population size. (GAVaPS). In the proposed strategy (assignment b...

En el cálculo de la constante de velocidad de absorción de primer orden para medicamentos que se comportan de acuerdo al modelo bicompartimental, es muy importante considerar algunas fuentes de error inherentes al mét...

Globally optimal triangulations are difficult to be found by deterministic methods as, for most type of criteria, no polynomial algorithm is known. In this work, we consider the Minimum Weight Triangulation (MWT) problem...

The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes ...

ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40-60-fold faster search and optimized model utiliz...

Se presenta una guía para resolver y estudiar modelos de expectativas racionales dinámicas lineales (LDRE). Luego de codificar el modelo, se aplica una function simple para log-linealizarlo; simular los efectos de seri...

Agents repesent a new paradigm for developing software applications. In spite of the interest of this particular way of looking at problems, there is considerable discrepancy on exactly what is an agent and which are the...

Scientific collaboration are becoming interdisciplinary, and scientists are working in informal collaboration to solve complex problems that require multiple types of large resources. An option is a computational grid. A...

The aqueous solubility of drugs/drug candidates (Sw) is one of the crucial physicochemical parameters in drug discovery studies and any computational method to predict the solubility is highly in demand in the pharmaceut...