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 …
An introduction to B‐cell epitope map** and in silico epitope prediction
L Potocnakova, M Bhide… - Journal of immunology …, 2016 - Wiley Online Library
Identification of B‐cell epitopes is a fundamental step for development of epitope‐based
vaccines, therapeutic antibodies, and diagnostic tools. Epitope‐based antibodies are …
vaccines, therapeutic antibodies, and diagnostic tools. Epitope‐based antibodies are …
Harnessing protein folding neural networks for peptide–protein docking
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
Engineered ACE2 receptor traps potently neutralize SARS-CoV-2
An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-
1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with …
1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with …
The Rosetta all-atom energy function for macromolecular modeling and design
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …
biological questions and engineering challenges ranging from interpretation of low …
Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses
EL Shrock, RT Timms, T Kula, EL Mena, AP West Jr… - Science, 2023 - science.org
Despite the vast diversity of the antibody repertoire, infected individuals often mount
antibody responses to precisely the same epitopes within antigens. The immunological …
antibody responses to precisely the same epitopes within antigens. The immunological …
Comparative ACE2 variation and primate COVID-19 risk
The emergence of SARS-CoV-2 has caused over a million human deaths and massive
global disruption. The viral infection may also represent a threat to our closest living …
global disruption. The viral infection may also represent a threat to our closest living …
Sequence co-evolution gives 3D contacts and structures of protein complexes
Protein–protein interactions are fundamental to many biological processes. Experimental
screens have identified tens of thousands of interactions, and structural biology has …
screens have identified tens of thousands of interactions, and structural biology has …
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations
Engineering stabilized proteins is a fundamental challenge in the development of industrial
and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph …
and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph …
Protein structure prediction and analysis using the Robetta server
Abstract The Robetta server (http://robetta. bakerlab. org) provides automated tools for
protein structure prediction and analysis. For structure prediction, sequences submitted to …
protein structure prediction and analysis. For structure prediction, sequences submitted to …