Table 2 presents a comparison of MAPPIS with two state-of-the art computational methods: Consurf [ 27], which calculates the evolutionary conservation within a protein family, and Robetta [ 14, 15], which explicitly calculates the expected change in the binding free energy upon mutation to alanine.
The mode-of-action was elucidated by applying the state-of-the-art computational methods (see the METHODS section for more details).
By providing an overview on state-of-the-art computational methods, we highlight the value of molecular modeling in mechanistically understanding TLR function and guiding drug design.
We further describe recent use of these methodologies to advance two separate drug discovery programs targeting acetyl-CoA carboxylase and tyrosine kinase 2. These examples suggest that tight integration of sophisticated chemistry teams with state-of-the-art computational methods can dramatically improve the efficiency of small molecule drug discovery.
Evolutionary biologist Russell Gray and his graduate student Quentin Atkinson of the University of Auckland in New Zealand combined state-of-the-art computational methods from evolutionary biology with an older technique for dating languages, called glottochronology.
The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases.
The data obtained in this work help to get a deeper insight in the potential and limitations of state-of-the-art computational methods used to complement NMR experiment interpretation for GAG molecules.
To facilitate the construction of workflows, we present XiP (eXtensible integrative Pipeline), a free [under the Lesser General Public License (LGPL)] and easy-to-use environment designed to integrate the state-of-the-art computational methods and to satisfy researchers' need in multi-collaborative projects.
Using the state-of-the-art computational method with the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, electronic, and optical properties were obtained, including band structures, density of states (DOSs), dielectric function, absorption coefficient, refractive index, energy loss function, and reflectivity.
The Model Building Algorithm (MBA), a current state-of-the-art computational method to build tissue-specific metabolic models, has been used to build liver, generic cancer, and two cancer cell line metabolic models thus far[ 14- 16].
