CryoPhold: CryoEM meets AlphaFold and molecular simulation to reveal protein dynamics
Bhakat S, Vats S, Mardt A, Strauch EM# · bioRxiv
Publications & software
Methods and molecular systems built to be used.
Selected publications and open computational resources from the lab. For a complete and current record, use Google Scholar, ORCID, or the WashU research profile.
Publications
Recent and foundational work.
Current work
Preprints and manuscripts in preparation
Peer-reviewed publications
2026
* Contributed equally · # Corresponding author
Accelerated sampling of protein dynamics using BioEmu augmented molecular simulation
Bhakat S, Strauch EM · Accepted in Journal of Chemical Information and Modeling · DOI: 10.1021/acs.jcim.6c01000 · bioRxiv version
ConforFold Recovers Alternative Protein Conformations Beyond MSA Subsampling
Syrlybaeva R, Strauch EM# · Protein Science · 9 April 2026
An intranasal adenoviral-vectored vaccine protects against highly pathogenic avian influenza H5N1 in naïve and antigen-experienced animals
Ying B, Pyles K, Darling TL, Seehra K, Pham T, Huang LC, Harastani HH, Sharma A, Desai P, Kashentseva EA, Curiel DT, Peters B, Case JB, Strauch EM, Diamond MS, Boon ACM · Cell Reports Medicine · 30 January 2026
Systematic computer-aided disulfide design as a general strategy to stabilize prefusion class I fusion proteins
Gonzalez KJ, Yim K, Boukhvalova MS, Kim S, Strauch EM# · Frontiers in Immunology · 2024 Jul 24;15:1406929
A general computational design strategy for stabilizing class I viral fusion proteins
Gonzalez KJ, Criado M, Huang J, Lei Y, Mousa JJ, Tompkins SM, Strauch EM# · Nature Communications · 2024 Feb 13;15:1335
Epitopes in the GPI signal peptide of Trypanosoma cruzi mucin proteins generate robust but delayed, nonprotective CD8+ T cell responses
Bunkofske ME, Perumal N, White BE, Strauch EM, Tarleton RL · Journal of Immunology · 2023
Sampling structure and sequence space of small protein folds
Linsky TW*, Noble K*, Tobin AR*, Crow R*, Carter L, Urbauer J, Baker D, Strauch EM# · Nature Communications · 2022 Nov 22;13:7151
Deep learning of protein sequence design of protein-protein interactions
Syrlybaeva R, Strauch EM# · Bioinformatics · 2022 Nov 15
Inhibition of a critical malaria host-pathogen interaction by a computationally designed inhibitor targeting Plasmodium vivax DBP
Tobin A*, Crow R*, Urusova D, Salinas ND, Carter L, Tolia NH, Strauch EM# · Protein Science · 2022
Robust de novo design of protein binding proteins from target structural information alone
Cao L*, Coventry B*, Goreshnik I, Huang B, Lee S, Jude K, Markovic I, Walsh STR, Bennett N, Phal AA, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, et al. · Nature · 2022 Mar 24
Large-scale design and refinement of stable proteins using sequence-only models
Singer JD#, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, et al. · PLoS ONE · 2022 Mar 14;17:e0265020
Decreased vaccine protection of egg-based influenza vaccine in the elderly could be associated with a non-hemagglutinin focused immunity
Gonzalez KJ, Strauch EM# · Journal of Clinical Investigation · 2021 Aug 2;131:e151732
Targeting viral surface proteins through structure-based design
Narkhede YB*, Gonzalez KJ*, Strauch EM# · Viruses · 2021;13:1320
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D · Science · 2020 Sep 9
Skp1 dimerization conceals its F-box protein binding site
Kim HW*, Eletsky A*, Gonzales KJ, van der Wel H, Strauch EM, Prestegard JH, West CM · Biochemistry · 2020 Apr 13
Parallelized identification of on- and off-target protein interactions
Dou J, Goreshnik I, Bryan C, Baker D, Strauch EM# · Molecular Systems Design & Engineering · 2019
An integrated device for the rapid and sensitive detection of the influenza hemagglutinin
Anderson CE, Buser JR, Fleming AM, Strauch EM, Ladd PD, Englund J, Baker D, Yager P · Lab on a Chip · 2019 Feb 26;19:885-896
Selected earlier work
Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site
Strauch EM, Bernard S, La D, Bohn A, Nieusma T, Lee P, Garcia NK, Holstein C, Anderson CE, Hooper KA, et al. · Nature Biotechnology · 2017 Jul;35:667-671
Development of a paper-based assay for whole influenza virus detection using a computationally designed hemagglutinin head region binder
Holstein CA*, Anderson CE*, Strauch EM, Bennett S, Chevalier A, Nelson J, Fu E, Baker D, Yager P · Analytical Chemistry · 2017 Jun 20;89:6608-6615
Multiplex pairwise assembly of array-derived DNA oligonucleotides
Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker B, Shendure J · Nucleic Acids Research · 2016 Mar 18;44:e43
Computational design of a pH-sensitive IgG binding protein
Strauch EM, Fleishman SJ, Baker D · Proceedings of the National Academy of Sciences · 2014 Jan 14;111:675-680
Open software
Code, models, and reproducible workflows.
Repositories are released through the Strauch Lab GitHub organization. These cards can be expanded as ASCENT and additional platforms mature.
github.com/strauchlab/iNNterfaceDesigniNNterfaceDesign
Deep-learning framework for one-sided sequence and motif design at protein–protein interfaces.
View repository →github.com/strauchlab/scaffold_designScaffold design
Design examples, protocols, and stability data for sampling diverse small protein folds.
View repository →github.com/strauchlab/cryoPholdCryoPhold
Bayesian reweighting of predicted structural ensembles against cryo-EM density to resolve protein dynamics.
View repository →github.com/strauchlab/ConforFoldConforFold
Protein conformational modeling for recovering alternative structures beyond MSA subsampling.
View repository →