Algorithms for protein design
Computational structure-based protein design programs are becoming an increasingly
important tool in molecular biology. These programs compute protein sequences that are …
important tool in molecular biology. These programs compute protein sequences that are …
[HTML][HTML] Strategies for designing non-natural enzymes and binders
The design of tailor-made enzymes is a major goal in biochemical research that can result in
wide-range applications and will lead to a better understanding of how proteins fold and …
wide-range applications and will lead to a better understanding of how proteins fold and …
OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
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 …
software. Osprey 3.0 features a convenient new Python interface, which greatly improves its …
BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large …
Computational protein design (CPD) algorithms that compute binding affinity, Ka, search for
sequences with an energetically favorable free energy of binding. Recent work shows that …
sequences with an energetically favorable free energy of binding. Recent work shows that …
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein …
The K* algorithm provably approximates partition functions for a set of states (eg, protein,
ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε …
ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε …
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Motivation When proteins mutate or bind to ligands, their backbones often move
significantly, especially in loop regions. Computational protein design algorithms must …
significantly, especially in loop regions. Computational protein design algorithms must …
LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency
Most protein design algorithms assume that the conformational space of proteins is discrete
and that their energy is residue-pairwise, ie, a sum of terms that depend on the sequence …
and that their energy is residue-pairwise, ie, a sum of terms that depend on the sequence …
iCFN: an efficient exact algorithm for multistate protein design
Motivation Multistate protein design addresses real-world challenges, such as multi-
specificity design and backbone flexibility, by considering both positive and negative protein …
specificity design and backbone flexibility, by considering both positive and negative protein …
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
Protein design algorithms that model continuous sidechain flexibility and conformational
ensembles better approximate the in vitro and in vivo behavior of proteins. The previous …
ensembles better approximate the in vitro and in vivo behavior of proteins. The previous …
(Branch and Bound over): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces
Protein design algorithms that compute binding affinity search for sequences with an
energetically favorable free energy of binding. Recent work shows that the following design …
energetically favorable free energy of binding. Recent work shows that the following design …