Publications
Beyond native sequence recovery: Improved modeling of the sequence-energy landscape of protein structures
Proc Natl Acad Sci USA, 2026
Training Bias and Sequence Alignments Shape Protein-Peptide Docking by AlphaFold and Related Methods
Protein Sci, 2025
Design of specific peptide inhibitors of toxin-antitoxin-mediated anti-phage defense
ACS Synth Biol, 2025
Elaboration of the Homer1 recognition landscape reveals incomplete divergence of paralogous EVH1 domains
Protein Sci, 2024
Jointly Embedding Protein Structures and Sequences through Residue Level Alignment
American Physical Society, 2024
PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions
Protein Sci, 2024
Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization
Structure, 2023
Marginal specificity in protein interactions constrains evolution of a paralogous family
Proc Natl Acad Sci USA, 2023
Tertiary motifs as building blocks for the design of protein-binding peptides
Protein Sci, 2022
Molecular determinants of TRAF6 binding specificity suggest that native interaction partners are not optimized for affinity
Protein Sci, 2022
Neural network-derived Potts models for structure-based protein design using backbone atomic coordinates and tertiary motifs
Protein Sci, 2022
A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers
eLife, 2021
Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP proteins
eLife, 2021
Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator
Neuron, 2020
Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics
Cell, 2020
Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1
Structure, 2019
PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode
Protein Sci, 2018
Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells
Proc Natl Acad Sci USA, 2018
Peptide design by optimization on a data-parameterized protein interaction landscape
Proc Natl Acad Sci USA, 2018
Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design
Methods Mol Biol, 2017
Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
eLife, 2017
Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1
eLife, 2017
Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils
Sci Rep, 2017
Generating High-Accuracy Peptide-Binding Data in High Throughput with Yeast Surface Display and SORTCERY
Methods Mol Biol, 2016
Selective peptide inhibitors of antiapoptotic cellular and viral Bcl-2 proteins lead to cytochrome c release during latent Kaposi's sarcoma-associated herpesvirus infection
Virus Res, 2016
The Orientations of Large Aspect-Ratio Coiled-Coil Proteins Attached to Gold Nanostructures
Small, 2016
Rapid Optimization of Mcl-1 Inhibitors using Stapled Peptide Libraries Including Non-Natural Side Chains
ACS Chem Biol, 2016
Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5
Protein Sci, 2016
Designing helical peptide inhibitors of protein-protein interactions
Curr Opin Struct Biol, 2016
AB-Bind: Antibody binding mutational database for computational affinity predictions
Protein Sci, 2016
Data-driven prediction and design of bZIP coiled-coil interactions
PLoS Comput Biol, 2015
Potent and specific peptide inhibitors of human pro-survival protein Bcl-xL
J Mol Biol, 2015
SORTCERY - A High-Throughput Method to Affinity Rank Peptide Ligands
J Mol Biol, 2015
Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins
J Mol Biol, 2015
A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy
ACS Synth Biol, 2015
Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins
PLoS Comput Biol, 2014
Increasing the affinity of selective bZIP-binding peptides through surface residue redesign
Protein Sci, 2014
Designed BH3 peptides with high affinity and specificity for targeting Mcl-1 in cells
ACS Chem Biol, 2014
A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit
J Am Chem Soc, 2014
bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans
Microbiology, 2013
Structure-based redesign of the binding specificity of anti-apoptotic Bcl-x(L)
J Mol Biol, 2013
Helix bundle loops determine whether histidine kinases autophosphorylate in cis or in trans
J Mol Biol, 2013
Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening
ACS Chem Biol, 2013
Networks of bZIP protein-protein interactions diversified over a billion years of evolution
Science, 2013
SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains
ACS Synth Biol, 2012
Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods
Protein Sci, 2012
In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2
Biochemistry, 2012
Predictive Bcl-2 family binding models rooted in experiment or structure
J Mol Biol, 2012
Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone
PLoS One, 2011
Design of peptide inhibitors that bind the bZIP domain of Epstein-Barr virus protein BZLF1
J Mol Biol, 2011
Determinants of homodimerization specificity in histidine kinases
J Mol Biol, 2011
Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes
Protein Sci, 2010
Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays
Biochemistry, 2010
Specific coiled-coil interactions contribute to a global model of the structure of the spindle pole body
J Struct Biol, 2010
A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering
J Am Chem Soc, 2010
Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL
J Mol Biol, 2010
The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer
Nat Chem Biol, 2010
Identifying and reducing error in cluster-expansion approximations of protein energies
J Comput Chem, 2010
Design of protein-interaction specificity gives selective bZIP-binding peptides
Nature, 2009
A computationally guided protein-interaction screen uncovers coiled-coil interactions involved in vesicular trafficking
J Mol Biol, 2009
X-ray vs. NMR structures as templates for computational protein design
Proteins, 2009
Structural specificity in coiled-coil interactions
Curr Opin Struct Biol, 2008
Analysis of coiled-coil interactions between core proteins of the spindle pole body
Biochemistry, 2008
Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL
J Mol Biol, 2007
Ultra-fast evaluation of protein energies directly from sequence
PLoS Comput Biol, 2006
Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure
Structure, 2005
AVID: an integrative framework for discovering functional relationships among proteins
BMC Bioinformatics, 2005
Orientation and oligomerization specificity of the Bcr coiled-coil oligomerization domain
Biochemistry, 2005
Predicting specificity in bZIP coiled-coil protein interactions
Genome Biol, 2004
Comprehensive identification of human bZIP interactions with coiled-coil arrays
Science, 2003