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Abstract The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2–6 . Here we des...

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...

In the search for new compounds for the treatment of Chagas disease, the cysteine protease cruzipain remains as one of the most attractive biomolecular targets for drug development. Thiosemicarbazones (TSCs) have been id...

Materias / palabras clave: Unix; Computer science; Data processing; Pipeline (software); Stream processing; Software; Asynchronous communication; Distributed computing; Database; Operating system; Computer network

The previously developed particle mesh Ewald method is reformulated in terms of efficient B-spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the ...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...