Stacey Gerben
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View article: Computational design of metalloproteases
Computational design of metalloproteases Open
Although significant progress has been made in creating de novo metalloenzymes that hydrolyze activated esters 1,2 , the energetically demanding cleavage of amide bonds has remained a major challenge for enzyme design: amide bonds are sign…
View article: De Novo Design of High‐Affinity Miniprotein Binders Targeting <i>Francisella Tularensis</i> Virulence Factor
De Novo Design of High‐Affinity Miniprotein Binders Targeting <i>Francisella Tularensis</i> Virulence Factor Open
Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection …
View article: De Novo Design of High‐Affinity Miniprotein Binders Targeting <i>Francisella Tularensis</i> Virulence Factor
De Novo Design of High‐Affinity Miniprotein Binders Targeting <i>Francisella Tularensis</i> Virulence Factor Open
Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection …
View article: Parametrically guided design of beta barrels and transmembrane nanopores using deep learning
Parametrically guided design of beta barrels and transmembrane nanopores using deep learning Open
Francis Crick’s global parameterization of coiled coil geometry has been widely useful for guiding design of new protein structures and functions. However, design guided by similar global parameterization of beta barrel structures has been…
View article: Diffusing protein binders to intrinsically disordered proteins
Diffusing protein binders to intrinsically disordered proteins Open
View article: De novo design of high-affinity miniprotein binders targeting Francisella tularensis virulence factor
De novo design of high-affinity miniprotein binders targeting Francisella tularensis virulence factor Open
Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella-like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection …
View article: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning
Accurate de novo design of high-affinity protein-binding macrocycles using deep learning Open
Developing macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no r…
View article: De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties
De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties Open
Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins can have considerable utility in regenerative medicine and next‐generation therapeutics. We use computational prot…
View article: Cyclic peptide structure prediction and design using AlphaFold2
Cyclic peptide structure prediction and design using AlphaFold2 Open
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training…
View article: Designed NGF mimetics with reduced nociceptive signatures in neurons
Designed NGF mimetics with reduced nociceptive signatures in neurons Open
The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75 NTR ; pain sensitization is thought…
View article: Design of high-affinity binders to immune modulating receptors for cancer immunotherapy
Design of high-affinity binders to immune modulating receptors for cancer immunotherapy Open
Immune receptors have emerged as critical therapeutic targets for cancer immunotherapy. Designed protein binders can have high affinity, modularity, and stability and hence could be attractive components of protein therapeutics directed ag…
View article: De novo designed proteins neutralize lethal snake venom toxins
De novo designed proteins neutralize lethal snake venom toxins Open
Snakebite envenoming remains a devastating and neglected tropical disease, claiming over 100,000 lives annually and causing severe complications and long-lasting disabilities for many more1,2. Three-finger toxins (3FTx) are high…
View article: Accurate<i>de novo</i>design of high-affinity protein binding macrocycles using deep learning
Accurate<i>de novo</i>design of high-affinity protein binding macrocycles using deep learning Open
The development of macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource-intensive and provide little control over binding mode. Despite considerable progress in physics-based metho…
View article: Publisher Correction: Multistate and functional protein design using RoseTTAFold sequence space diffusion
Publisher Correction: Multistate and functional protein design using RoseTTAFold sequence space diffusion Open
View article: Multistate and functional protein design using RoseTTAFold sequence space diffusion
Multistate and functional protein design using RoseTTAFold sequence space diffusion Open
View article: Designed endocytosis-inducing proteins degrade targets and amplify signals
Designed endocytosis-inducing proteins degrade targets and amplify signals Open
View article: De novo Design of Near Infrared Fluorescent Proteins
De novo Design of Near Infrared Fluorescent Proteins Open
Fluorescent proteins have revolutionized the field of molecular imaging, enabling the visualization of diverse biological processes. Biological imaging in the near-infrared (NIR, 800-1000 nm) and shortwave infrared (SWIR, 1000-2000 nm) ran…
View article: Parametrically guided design of beta barrels and transmembrane nanopores using deep learning
Parametrically guided design of beta barrels and transmembrane nanopores using deep learning Open
Francis Crick’s global parameterization of coiled coil geometry has been widely useful for guiding design of new protein structures and functions. However, design guided by similar global parameterization of beta barrel structures has been…
View article: Diffusing protein binders to intrinsically disordered proteins
Diffusing protein binders to intrinsically disordered proteins Open
Proteins which bind intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could have considerable utility for therapeutic and diagnostic applications. However, a general met…
View article: Design of intrinsically disordered region binding proteins
Design of intrinsically disordered region binding proteins Open
Intrinsically disordered proteins and peptides play key roles in biology, but the lack of defined structures and the high variability in sequence and conformational preferences has made targeting such systems challenging. We describe a gen…
View article: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies Open
Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cas…
View article: De novo designed proteins neutralize lethal snake venom toxins
De novo designed proteins neutralize lethal snake venom toxins Open
View article: Design of High Affinity Binders to Convex Protein Target Sites
Design of High Affinity Binders to Convex Protein Target Sites Open
While there has been progress in the de novo design of small globular miniproteins (50-65 residues) to bind to primarily concave regions of a target protein surface, computational design of minibinders to convex binding sites remains an ou…
View article: De novo design of high-affinity binders of bioactive helical peptides
De novo design of high-affinity binders of bioactive helical peptides Open
View article: Designed Endocytosis-Triggering Proteins mediate Targeted Degradation
Designed Endocytosis-Triggering Proteins mediate Targeted Degradation Open
Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by interaction with endogenous ligands. Therapeutic approaches such as LYTAC 1,2 and KineTAC 3 , have taken advantage of this to target specific proteins for …
View article: Design of stimulus-responsive two-state hinge proteins
Design of stimulus-responsive two-state hinge proteins Open
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing…
View article: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies Open
Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. …
View article: Design of stimulus-responsive two-state hinge proteins
Design of stimulus-responsive two-state hinge proteins Open
Proteins that switch between two structural states as a function of environmental stimuli are widespread in nature. These proteins structurally transduce biochemical information in a manner analogous to how transistors control information …
View article: Design of Diverse Asymmetric Pockets in <i>De Novo</i> Homo-oligomeric Proteins
Design of Diverse Asymmetric Pockets in <i>De Novo</i> Homo-oligomeric Proteins Open
A challenge for design of protein-small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcom…
View article: De novo design of transmembrane β barrels
De novo design of transmembrane β barrels Open
Building a barrel Computational design offers the possibility of making proteins with customized structures and functions. The range of accessible protein scaffolds has expanded with the design of increasingly complex cytoplasmic proteins …