GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations [0.03%]
GENESIS：一种用于生物分子和细胞模拟的混合并行及多尺度分子动力学模拟器，并带有增强采样算法
Jaewoon Jung,Takaharu Mori,Chigusa Kobayashi et al.
Jaewoon Jung et al.
GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition a...
The topology of fullerenes [0.03%]
富勒烯的拓扑学
Peter Schwerdtfeger,Lukas N Wirz,James Avery
Peter Schwerdtfeger
Fullerenes are carbon molecules that form polyhedral cages. Their bond structures are exactly the planar cubic graphs that have only pentagon and hexagon faces. Strikingly, a number of chemical properties of a fullerene can be derived from ...
Carbohydrate force fields [0.03%]
碳水化合物力场
B Lachele Foley,Matthew B Tessier,Robert J Woods
B Lachele Foley
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their ele...
Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions [0.03%]
用于模拟凝聚相反应的量子力学/分子力学(MC方法
Orlando Acevedo,Wiliiam L Jorgensen
Orlando Acevedo
A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical...
Kestutis Aidas,Celestino Angeli,Keld L Bak et al.
Kestutis Aidas et al.
Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster ...
Helgi I Ingólfsson,Cesar A Lopez,Jaakko J Uusitalo et al.
Helgi I Ingólfsson et al.
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-...
John B O Mitchell
John B O Mitchell
Machine learning algorithms are generally developed in computer science or adjacent disciplines and find their way into chemical modeling by a process of diffusion. Though particular machine learning methods are popular in chemoinformatics ...
Jörg Neugebauer,Tilmann Hickel
Jörg Neugebauer
Materials science is a highly interdisciplinary field. It is devoted to the understanding of the relationship between (a) fundamental physical and chemical properties governing processes at the atomistic scale with (b) typically macroscopic...
Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance [0.03%]
化学生物信息学和语义网：利用链接数据和增强式过程增加价值
Jeremy G Frey,Colin L Bird
Jeremy G Frey
Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject o...
Rajarshi Guha
Rajarshi Guha
In this article we present an overview of the origin and applications of the activity landscape view of structure-actvitiy relationship data as conceived by Maggiora. Within this landscape, different regions exemplify different aspects of S...