YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations

TL;DR: In this paper, the authors evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD.

TL;DR: To establish the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measure virus-specific CD4+ and CD8+ T cells, epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases are studied.

TL;DR: A comprehensive predictive framework is adapted to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19.

TL;DR: This review takes the reader in a journey of exploration from the beginnings to the most recent turnabouts, which have revolutionized the field of homology modeling, and discusses the new trends emerging in this rapidly growing field.

TL;DR: A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST and achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date.

TL;DR: The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.

TL;DR: The root mean square deviation in the positions of the main chain atoms, delta, is related to the fraction of mutated residues, H, by the expression: delta(A) = 0.40 e1.87H.

TL;DR: In this article, the authors introduce the concept of Computational Quantum Mechanics (CQM) and present four challenges in molecular modelling: Free Energies, Solvation, Reactions and Solid-State Defects.