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Amber 2023
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the ...
Amber 2021
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are di...
Advances in Bioinformatics and Computational Biology
This book constitutes the refereed proceedings of the Brazilian Symposium on Bioinformatics, BSB 2005, held in Sao Leopoldo, Brazil in July 2005. The 15 revised full papers and 10 revised extended abstracts presented together with 3 invited papers were carefully reviewed and selected from 55 submissions. The papers address a broad range of current topics in computational biology and bioinformatics.
Annual Reports in Computational Chemistry
Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry. * Broad coverage of computational chemistry and up-to-date information * Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings * Each chapter reviews the most recent literature on a specific topic of interest to computational chemists
Amber 2022
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are di...
Parallel Computing: Technology Trends
The year 2019 marked four decades of cluster computing, a history that began in 1979 when the first cluster systems using Components Off The Shelf (COTS) became operational. This achievement resulted in a rapidly growing interest in affordable parallel computing for solving compute intensive and large scale problems. It also directly lead to the founding of the Parco conference series. Starting in 1983, the International Conference on Parallel Computing, ParCo, has long been a leading venue for discussions of important developments, applications, and future trends in cluster computing, parallel computing, and high-performance computing. ParCo2019, held in Prague, Czech Republic, from 10 – ...
Modeling Solvent Environments
A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
Advances in Bioinformatics and Computational Biology
This book constitutes the refereed proceedings of the 8th Brazilian Symposium on Bioinformatics, BSB 2013, held in Recife, Brazil, in November 2013. The 18 regular papers presented were carefully reviewed and selected for inclusion in this book. The papers cover all aspects of bioinformatics and computational biology.
