Anna U. Lowegard
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View article: Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design
Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design Open
Broadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth and potency of neutralization. We employ the OSPREY computational protein design …
View article: Early computational detection of potential high-risk SARS-CoV-2 variants
Early computational detection of potential high-risk SARS-CoV-2 variants Open
The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants daily. While most variants do not impact the course of the pandemic, some variants pose an increased risk when the acquired mutations allow …
View article: Early Computational Detection of Potential High Risk SARS-CoV-2 Variants
Early Computational Detection of Potential High Risk SARS-CoV-2 Variants Open
The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants on a daily basis. While most variants do not impact the course of the pandemic, some variants pose a significantly increased risk when the a…
View article: Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface Open
The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε-approximation for a particular set of partition functio…
View article: Minimization-Aware Recursive <i>K*:</i> A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
Minimization-Aware Recursive <i>K*:</i> A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape Open
Protein design algorithms that model continuous sidechain flexibility and conformational ensembles better approximate the in vitro and in vivo behavior of proteins. The previous state of the art, iMinDEE-A*-K*, computes provable ɛ-approxim…
View article: Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface Open
The K * algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε . Often, reaching an ε -approximation for a particular set of partition func…
View article: Replication Data for Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface
Replication Data for Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface Open
These files contain all of the necessary code to re-create the results in the manuscript entitled "Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:…
View article: Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand
Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand Open
PDZ domains are small protein-binding domains that interact with short, mostly C-terminal peptides and play important roles in cellular signaling and the trafficking and localization of ion channels. The CFTR-associated ligand PDZ domain (…
View article: OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
OSPREY 3.0: Open‐source protein redesign for you, with powerful new features Open
We present osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than …
View article: OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features
OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features Open
We present OSPREY 3.0, a new and greatly improved release of the OSPREY protein design software. OSPREY 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than …