Related papers: FreeSASA: An open source C library for solvent acc…
In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to…
FlexibleSUSY is a software package that takes as input descriptions of (non-)minimal supersymmetric models written in Wolfram/Mathematica and generates a set of spectrum generator libraries and executables, with the aid of SARAH. The design…
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue…
JISA is a software library, written in Java, aimed at providing an easy, flexible and standardised means of creating experimental control software for physical sciences researchers. Specifically, with an emphasis on enabling measurement…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
The ability of snapshot compressive imaging (SCI) systems to efficiently capture high-dimensional (HD) data depends on the advent of novel optical designs to sample the HD data as two-dimensional (2D) compressed measurements. Nonetheless,…
SOL is an open-source library for scalable online learning algorithms, and is particularly suitable for learning with high-dimensional data. The library provides a family of regular and sparse online learning algorithms for large-scale…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To…
With "contact surface area" (CSA) we refers to the area of contact between a tumor and an organ. This indicator has been identified as a predictive factor for surgical peri-operative parameters, particularly in the context of kidney cancer.…
Usability evaluation has received considerable attention from both the research and practice communities. While there are many evaluation tools available, the Software Usability Scale (SUS) is the most widely used. In this paper, we…
The sensitivity analysis and validation of simulation models require specific approaches in the case of spatial models. We describe the spatialdata scala library providing such tools, including synthetic generators for urban configurations…
The library of practical abstractions (LIBPA) provides efficient implementations of conceptually simple abstractions, in the C programming language. We believe that the best library code is conceptually simple so that it will be easily…
Adaptive simulated annealing (ASA) is a global optimization algorithm based on an associated proof that the parameter space can be sampled much more efficiently than by using other previous simulated annealing algorithms. The author's ASA…
SOFTSUSY is a program which accurately calculates the spectrum of superparticles in the CP-conserving Minimal Supersymmetric Standard Model (MSSM), with a full flavour mixing structure. The program solves the renormalisation group equations…
\texttt{rCOSA} is a software package interfaced to the R language. It implements statistical techniques for clustering objects on subsets of attributes in multivariate data. The main output of COSA is a dissimilarity matrix that one can…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
The R software has become popular among researchers due to its flexibility and open-source nature. However, researchers in the fields of public health and epidemiological studies are more customary to commercial statistical softwares such…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
PCMSolver is an open-source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver…