OSPREY 3.0: Open-source protein redesign for you, with powerful new features

Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity

(2017) Gwo-Yu Chuang et al.   JOURNAL OF VIROLOGY

A critical analysis of computational protein design with sparse residue interaction graphs

(2017) Swati Jain et al.   PLoS Computational Biology

Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting

(2017) Nicole A. Doria-Rose et al.   PLoS Pathogens

Algorithms for protein design

(2016) Pablo Gainza et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design

(2016) Yuchao Pan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design

(2016) Jonathan D. Jou et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

comets(Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence

(2016) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads

(2015) Regina S. Salvat et al.   BIOTECHNOLOGY AND BIOENGINEERING

Depletion of T Cell Epitopes in Lysostaphin Mitigates Anti-Drug Antibody Response and Enhances Antibacterial Efficacy In Vivo

(2015) Hongliang Zhao et al.   CHEMISTRY & BIOLOGY

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design

(2015) Mark A. Hallen et al.   Journal of Chemical Theory and Computation

Fast gap-free enumeration of conformations and sequences for protein design

(2015) Kyle E. Roberts et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein design algorithms predict viable resistance to an experimental antifolate

(2015) Stephanie M. Reeve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An efficient parallel algorithm for accelerating computational protein design

(2014) Yichao Zhou et al.   BIOINFORMATICS

Antibodies VRC01 and 10E8 Neutralize HIV-1 with High Breadth and Potency Even with Ig-Framework Regions Substantially Reverted to Germline

(2014) I. S. Georgiev et al.   JOURNAL OF IMMUNOLOGY

Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo

(2014) R. S. Rudicell et al.   JOURNAL OF VIROLOGY

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Structure-Guided Deimmunization of Therapeutic Proteins

(2013) Andrew S. Parker et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

(2013) Mark A. Hallen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design of epitope-specific probes for sera analysis and antibody isolation

(2012) I Georgiev et al.   Retrovirology

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

(2012) Kyle E. Roberts et al.   PLoS Computational Biology

Protein Design Using Continuous Rotamers

(2012) Pablo Gainza et al.   PLoS Computational Biology

Structural Linkage between Ligand Discrimination and Receptor Activation by Type I Interferons

(2011) Christoph Thomas et al.   CELL

Computational structure-based redesign of enzyme activity

(2009) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algorithm for backrub motions in protein design

(2008) I. Georgiev et al.   BIOINFORMATICS

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

(2008) Ivelin Georgiev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains

(2008) R. J. Bingham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA