Protein design: From the aspect of water solubility and stability
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …
sequence and 3D-conformation. Their manipulation represents important aspects of the …
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …
With the increasing amount and complexity of data, scalability and reproducibility have …
Macromolecular modeling and design in Rosetta: recent methods and frameworks
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …
in laboratories worldwide. During two decades of development by a community of …
The openCARP simulation environment for cardiac electrophysiology
Abstract Background and Objective: Cardiac electrophysiology is a medical specialty with a
long and rich tradition of computational modeling. Nevertheless, no community standard for …
long and rich tradition of computational modeling. Nevertheless, no community standard for …
A brief history of de novo protein design: minimal, rational, and computational
DN Woolfson - Journal of Molecular Biology, 2021 - Elsevier
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the
primary motivation for de novo protein design was to test our understanding of the …
primary motivation for de novo protein design was to test our understanding of the …
[HTML][HTML] Homology modeling in the time of collective and artificial intelligence
Homology modeling is a method for building protein 3D structures using protein primary
sequence and utilizing prior knowledge gained from structural similarities with other …
sequence and utilizing prior knowledge gained from structural similarities with other …
Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens
The design of new biomolecules able to harness immune mechanisms for the treatment of
diseases is a prime challenge for computational and simulative approaches. For instance, in …
diseases is a prime challenge for computational and simulative approaches. For instance, in …
Modeling immunity with Rosetta: methods for antibody and antigen design
Structure-based antibody and antigen design has advanced greatly in recent years, due not
only to the increasing availability of experimentally determined structures but also to …
only to the increasing availability of experimentally determined structures but also to …
General purpose structure-based drug discovery neural network score functions with human-interpretable pharmacophore maps
BP Brown, J Mendenhall, AR Geanes… - Journal of chemical …, 2021 - ACS Publications
The BioChemical Library (BCL) is an academic open-source cheminformatics toolkit
comprising ligand-based virtual high-throughput screening (vHTS) tools such as quantitative …
comprising ligand-based virtual high-throughput screening (vHTS) tools such as quantitative …
[HTML][HTML] SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate …
S Aramyan, K McGregor, S Sandeep… - Frontiers in …, 2022 - frontiersin.org
The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective
collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and …
collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and …