Peer Review

Peer review of scientific manuscripts is essential for what is, currently, by far the most widely accepted means of communication of scientific results: publishing papers in scientific journals. The process of peer review plays an important role in refining the body of work prior to final publication.

We believe that transparency in peer review can improve the speed, quality, and collegiality of the publication process. Peer review is also an important training opportunity for lab members in scientific thinking and writing. As such, we only review manuscripts that have been posted on preprint servers and we post our peer review comments publicly. Additional resources can be found in our Lab Compact and in the Peer Review minicourse. We support other initiatives to improve peer review (such as Review Commons and FeedbackASAP).

On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells

Picco G, Rao Y, Al Saedi A, Walker SJ, Bhosle S, Lee Y, Vieira SF, Garcia-Casado M, Valdes Garcia G, May K, Sassi F, Barrio Hernandez I, Sharma M, Dincer C, Bell T, Kavasakali A, Shenje R, Martyr C, Brnardic E, Deng N, Grigorova Dimitrova H, Karakoc E, Sundara Rajan S, Chan N, Hitch E, McCarten K, Fourneaux C, Hewitson Z, Lightfoot H, Barthorpe S, Phelan JP, Landis P, Jones B, Munoz D, Prakash J, Barsanti P, Taygerly J, DeMartino MP, Gonçalves E, Bertotti A, Trusolino L, White M, Sharma G, Coelho MA, Houseley J, Schwartz B, Garnett MJ.


Reviewed by: Fraser JS, Bali S. - June 2026


Figure from On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells

Peer Review


Anticipating on-target resistance to WRN inhibitors in microsatellite unstable cancers

Orcholski ME, Laterreur N, Masud W, Shenoy S, Chapdelaine-Trépanier V, Bowlan J, Minju-OP A, Cabré-Romans JJ, Sack T, Fiore C, Young JTF, Álvarez-Quilón A, Cuella-Martin R.


Reviewed by: Fraser JS, Bali S. - June 2026


Figure from Anticipating on-target resistance to WRN inhibitors in microsatellite unstable cancers

Peer Review


Density-guided AlphaFold3 uncovers unmodelled conformations in β2-microglobulin

Maddipatla A, Vedula S, Bronstein AM, Marx A.


Reviewed by: Chrispens K, Lyubimov A, Fraser JS. - May 2026


Figure from Density-guided AlphaFold3 uncovers unmodelled conformations in β2-microglobulin

Peer Review


De novo design of protein nanoparticles with integrated functional motifs

Haas CM, Rankovic S, Lewis HK, Carr KD, Weidle C, Gerdes SS, Nuss LR, Ruiz F, Moiz S, Fiorelli M, Grey E, McGowan J, Kumar N, Creanga A, Kang A, Nguyen H, Wang Y, Sankaran B, Dosey A, Ravichandran R, Bera AK, Leaf EM, DeForest CA, Kanekiyo M, Borst AJ, King NP.


Reviewed by: Shvareva V, Olavarrieta Colasurdo A, Fraser JS, Cheung B. - May 2026


Figure from De novo design of protein nanoparticles with integrated functional motifs

Peer Review


Towards pharmacokinetic profile predictions for monoclonal antibodies using sequence based machine learning derived parameters and compartmental modeling

Jost F, Cordes H.


Reviewed by: Frazier J, Asencor A, Fraser JS, Cheung B. - May 2026


Figure from Towards pharmacokinetic profile predictions for monoclonal antibodies using sequence based machine learning derived parameters and compartmental modeling

Peer Review


Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

Berman DS, Lewis LM, Curtis TD, Tiburzi ON, Smith DFQ, Casadevall A, Dunphy LJ.


Reviewed by: Perez B, Abdoli P, Fraser JS, Cheung B. - May 2026


Figure from Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

Peer Review


TissueFormer: Extending single-cell foundation models to predict population-level phenotypes

Benjamin AS, Zador A.


Reviewed by: Oberhauser J, Nag B, Fraser JS, Cheung B. - May 2026


Figure from TissueFormer: Extending single-cell foundation models to predict population-level phenotypes

Peer Review


Zero-shot design of a de novo metalloenzyme

El Nesr G, Dürr SL, Mathews II, Wen Q, Zhao K, Sarangi R, Röthlisberger U, Sunden F, Huang PS.


Reviewed by: Lonnquist B, Fillion A, Fraser JS, Cheung B. - May 2026


Figure from Zero-shot design of a de novo metalloenzyme

Peer Review


DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

Liu Z, Sun H, Wang Y, Ren Y, Rao L, Huang Z, Cao H, Hu X, Zhu X, Li M, Wan J.


Reviewed by: Fraser JS, Zou Z. - March 2026


Figure from DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

Peer Review


PathDiffusion: modeling protein folding pathway using evolution-guided diffusion

Zhao K, Xiang C, Cheng B, Shen Y, Wang W, Chen S, Su B, Zhang G, Peng Z, Yang J.


Reviewed by: Tong A, Bali S, Fraser JS. - February 2026


Figure from PathDiffusion: modeling protein folding pathway using evolution-guided diffusion

Peer Review


X-ray Crystallography-Guided Design and Synthesis of Cyclopentyl Heteroaryl Carboxylic Acid based Inhibitors of the SARS-CoV-2 Nsp3 Macrodomain (Mac1)

Wang X, Butler WTW, Donald JR, Wang Y, Shaw AL, Schuller M, Fearon D, Aschenbrenner JC, Marples PG, Watt G, Lucas SCC, Bonomo S, Nelson JE, Ahel I, Von Delft F, O’Brien P.


Reviewed by: Fraser JS, Walters WP. - February 2026


Figure from X-ray Crystallography-Guided Design and Synthesis of Cyclopentyl Heteroaryl Carboxylic Acid based Inhibitors of the SARS-CoV-2 Nsp3 Macrodomain (Mac1)

Peer Review


Generative design of novel bacteriophages with genome language models

King SH, Driscoll CL, Lii DB, Guo D, Merchant AT, Brixi G, Wilkinson ME, Hie BL.


Reviewed by: Fraser JS, Bondy-Denomy J. - September 2025


Figure from Generative design of novel bacteriophages with genome language models

Peer Review


AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

Fadini A, Li M, McCoy AJ, Terwilliger TC, Read RJ, Hekstra D, AlQuraishi M.


Reviewed by: Fraser JS, Wankowicz SA, Chrispens KM. - July 2025


Figure from AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

Peer Review


Conserved energetic changes drive function in an ancient protein fold

Wells ML, Lu C, Sultanov D, Weber KC, Gong Z, Glasgow A.


Reviewed by: Kim G, Rao J, Fraser JS, Anonymous Student. - July 2025


Figure from Conserved energetic changes drive function in an ancient protein fold

Peer Review


Have protein-ligand co-folding methods moved beyond memorisation?

Škrinjar P, Eberhardt J, Durairaj J, Schwede T.


Reviewed by: Chrispens KM, Hazelwood I, Fraser JS. - June 2025


Figure from Have protein-ligand co-folding methods moved beyond memorisation?

Peer Review


Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

Passaro S*, Corso G*, Wohlwend J*, Reveiz M*, Thaler S*, Somnath VR, Getz N, Portnoi T, Roy J, Stark H, Kwabi-Addo D, Beaini D, Jaakkola T, Barzilay R.


Reviewed by: Chrispens KM, Wankowicz SA, Fraser JS. - June 2025


Figure from Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

Peer Review


Oligomerization enables the selective targeting of intrinisically disordered regions by small molecules

Bielskutė S, Mateos B, Awawdy M, Garcia-Cabau C, Niskanen H, Sánchez-Zarzalejo C, Bracaglia L, Pierattelli R, Felli IC, Frigolé-Vivas M, García J, Riera A, Hnisz D, Salvatellay X.


Reviewed by: Gupta NG, Fraser JS, Coyote-Maestas W, Anonymous Student. - June 2025


Figure from Oligomerization enables the selective targeting of intrinisically disordered regions by small molecules

Peer Review


Energetic and structural control of polyspecificity in a multidrug transporter

Miller ST, Henzler-Wildman KA, Raman S.


Reviewed by: Hazelwood I, Fraser JS, Coyote-Maestas W, Anonymous Student. - May 2025


Figure from Energetic and structural control of polyspecificity in a multidrug transporter

Peer Review


InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Simon E, Zou J.


Reviewed by: Chrispens KM, Fraser JS. - January 2025


Figure from InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Peer Review


Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding

Singh S, Gapsys V, Aldeghi M, Schaller D, Rangwala AM, White JB, Bluck JP, Scheen J, Glass WG, Guo J, Hayat S, de Groot BL, Volkamer A, Christ CD, Seeliger MA, Chodera JD.


Reviewed by: Zou Z, Mitra R, Fraser JS. - December 2024


Figure from Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding

Peer Review


Computational design of highly active de novo enzymes

Braun M, Tripp A, Chakatok M, Kaltenbrunner S, Totaro M, Stoll D, Bijelic A, Elaily W, Hoch SY, Aleotti M, Hall M, Oberdorfer G.


Reviewed by: Mitra R, Bajaj P, Fraser JS. - December 2024


Figure from Computational design of highly active de novo enzymes

Peer Review


Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

Astore MA, Blackwell R, Silva-Sánchez D, Cossio P, Hanson SM.


Reviewed by: San Felipe CJ, Flowers J, Fraser JS. - December 2024


Figure from Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

Peer Review


Seeing Double: Molecular dynamics simulations reveal the stability of certain alternate protein conformations in crystal structures

Rosenberg AA, Vedula S, Bronstein AM, Marx A.


Reviewed by: Flowers J, Gupta N, Fraser JS. - December 2024


Figure from Seeing Double: Molecular dynamics simulations reveal the stability of certain alternate protein conformations in crystal structures

Peer Review


Effects of residue substitutions on the cellular abundance of proteins

Schulze TK, Lindorff-Larsen K.


Reviewed by: Zou Z, Fraser JS. - October 2024


Figure from Effects of residue substitutions on the cellular abundance of proteins

Peer Review


Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations

Posani E, Janoš P, Haack D, Toor N, Bonomi M, Magistrato A, Bussi G.


Reviewed by: Raskar T, Lee S, Fraser JS. - October 2024


Figure from Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations

Peer Review


Energetic portrait of the amyloid beta nucleation transition state

Arutyunyan A, Seuma M, Faure AJ, Bolognesi B, Lehner B.


Reviewed by: Samelson A, Fraser JS. - September 2024


Figure from Energetic portrait of the amyloid beta nucleation transition state

Peer Review


Bioorthogonal labeling of chitin in pathogenic Candida species reveals biochemical mechanisms of hyphal growth and homeostasis

Williams C, Carnahan BR, Hyland SN, Grimes CL.


Reviewed by: Fraser JS. - September 2024


Figure from Bioorthogonal labeling of chitin in pathogenic Candida species reveals biochemical mechanisms of hyphal growth and homeostasis

Peer Review


Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography

Schulz EC, Prester A, von Stetten D, Gore G, Hatton CE, Bartels K, Leimkohl JP, Schikora H, Ginn HM, Tellkamp F, Mehrabi P.


Reviewed by: Fraser JS. - September 2024


Figure from Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography

Peer Review


Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron

Zielinski KA, Dolamore C, Dalton KM, Smith N, Termini J, Henning R, Srajer V, Hekstra DR, Pollack L, Wilson MA.


Reviewed by: Asthana P, Correy GJ, Fraser JS. - September 2024


Figure from Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron

Peer Review


Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex

Patel A, Sinha S, Arantes P, Palermo G.


Reviewed by: Chen D, Flowers J, Fraser JS. - September 2024


Figure from Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex

Peer Review


FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking

Vincoff S, Goel S, Kholina K, Pulugurta R, Vure P, Chatterjee P.


Reviewed by: Bajaj P, Macdonald CB. - July 2024


Figure from FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking

Peer Review


A complete map of specificity encoding for a partially fuzzy protein interaction

Zarin T, Lehner B.


Reviewed by: Krupkin B, Le M, Coyote-Maestas W, Fraser JS. - June 2024


Figure from A complete map of specificity encoding for a partially fuzzy protein interaction

Peer Review


Dissecting translation elongation dynamics through ultra-long tracking of single ribosomes

Madern MF, Yang S, Witteveen O, Bauer M, Tanenbaum ME.


Reviewed by: Chen Y, Student 1, Student 2, Coyote-Maestas W, Fraser JS. - May 2024


Figure from Dissecting translation elongation dynamics through ultra-long tracking of single ribosomes

Peer Review


Highly multiplexed design of an allosteric transcription factor to sense novel ligands

Nishikawa KK, Chen J, Acheson JF, Harbaugh SV, Huss P, Frenkel M, Novy N, Sieren HR, Lodewyk EC, Lee DH, Chávez JL, Fox BG, Raman S.


Reviewed by: Mullin-Bernstein Z, Chrispens K, Coyote-Maestas W, Fraser JS. - May 2024


Figure from Highly multiplexed design of an allosteric transcription factor to sense novel ligands

Peer Review


Targeting protein-ligand neosurfaces using a generalizable deep learning approach

Marchand A, Buckley S, Schneuing A, Pacesa M, Gainza P, Elizarova E, Neeser RM, Lee PW, Reymond L, Elia M, Scheller L, Georgeon S, Schmidt J, Schwaller P, Maerkl SJ, Bronstein M, Correia BE.


Reviewed by: Chen MN, Alamo KAE, Coyote-Maestas W, Fraser JS. - May 2024


Figure from Targeting protein-ligand neosurfaces using a generalizable deep learning approach

Peer Review


Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape

Wu X, Go M, Nguyen JV, Kuchel NW, Lu BG, Lowes KN, Calleja DJ, Mitchell JP, Lessene G, Komander D, Call ME.


Reviewed by: Bajaj P, Fraser JS. - May 2024


Figure from Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape

Peer Review


Heterogeneous folding landscapes and predetermined breaking points within a protein family

Pechmann S.


Reviewed by: Macdonald CB and San Felipe CJ. - April 2024


Figure from Heterogeneous folding landscapes and predetermined breaking points within a protein family

Peer Review


AlphaFold Meets Flow Matching for Generating Protein Ensembles

Jing B, Berger B, Jaakkola T.


Reviewed by: Jansen F, Ravikumar A, Wankowicz SA, Fraser JS. - April 2024


Figure from AlphaFold Meets Flow Matching for Generating Protein Ensembles

Peer Review


Prediction of Ca 2+ binding site in proteins with a fast and accurate method based on statistical mechanics and analysis of crystal structures

Basit A, Choudhury D, Bandyopadhyay P.


Reviewed by: Wankowicz SA. - April 2024


Figure from Prediction of Ca 2+ binding site in proteins with a fast and accurate method based on statistical mechanics and analysis of crystal structures

Peer Review


Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death

Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK.


Reviewed by: Yamamura H, Mitra R, Fraser JS. - April 2024


Figure from Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death

Peer Review


Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures

Shub L, Liu W, Skiniotis G, Keiser M, Robertson M.


Reviewed by: Wankowicz SA. - April 2024


Figure from Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures

Peer Review


Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

Ke Z, Peacock TP, Brown JC, Sheppard CM, Croll TI, Kotecha A, Goldhill DH, Barclay WS, Briggs JAG.


Reviewed by: Fraser JS, HHMI TAP participants. - March 2024


Figure from Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

Peer Review


High-throughput computational discovery of inhibitory protein fragments with AlphaFold

Savinov A, Swanson S, Keating AE, Li GW.


Reviewed by: San Felipe CJ, Bajaj P, Fraser JS. - February 2024


Figure from High-throughput computational discovery of inhibitory protein fragments with AlphaFold

Peer Review


Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane

González-López A, Larsson DSD, Koripella RK, Cain BN, Chavez MG, Hergenrother PJ, Sanyal S, Selmer M.


Reviewed by: Dandan M, Chen D, Fraser JS. - February 2024


Figure from Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane

Peer Review


Exploring serial crystallography for drug discovery

Dunge A, Phan C, Uwangue O, Bjelcic M, Gunnarsson J, Wehlander G, Käck H, Brändén G.


Reviewed by: Fraser JS. - December 2023


Figure from Exploring serial crystallography for drug discovery

Peer Review


Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Topolska M, Beltran A, Lehner B.


Reviewed by: Bajaj P, Chrispens K, Fraser JS, Coyote-Maestas W. - November 2023


Figure from Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Peer Review


MatchMaps: Non-isomorphous difference maps for X-ray crystallography

Brookner DE, Hekstra DR.


Reviewed by: Asthana P, Correy GJ, Fraser JS. - November 2023


Figure from MatchMaps: Non-isomorphous difference maps for X-ray crystallography

Peer Review


Approximating conformational Boltzmann distributions with AlphaFold2 predictions

Brown BP, Stein RA, Meiler J, Mchaourab H.


Reviewed by: Flowers J, Lam A, Ravikumar A, Fraser J. - October 2023


Figure from Approximating conformational Boltzmann distributions with AlphaFold2 predictions

Peer Review


Detuning of the Ribosome Conformational Landscape Promotes Antibiotic Resistance and Collateral Sensitivity

Mesa P, Jiménez-Fernández A, La Rosa R, Espinosa R, Johansen HK, Molin S, Montoya G.


Reviewed by: Raskar T, Dandan M, Fraser JS. - September 2023


Figure from Detuning of the Ribosome Conformational Landscape Promotes Antibiotic Resistance and Collateral Sensitivity

Peer Review


Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Walker EJ, Hamill CJ, Crean R, Connolly MS, Warrender AK, Kraakman KL, Prentice EJ, Steyn-Ross A, Steyn-Ross M, Pudney CR, van der Kamp MW, Schipper LA, Mulholland AJ, Arcus VL..


Reviewed by: Chen D, Muir D, Pinney M, Fraser JS. - August 2023


Figure from Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Peer Review


Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2

da Silva GM, Cui JY, Dalgarno DC, Lisi GP, Rubenstein BM.


Reviewed by: Ravikumar A, Lee S, Fraser Lab. - August 2023


Figure from Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2

Peer Review

Author response

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Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase

Coricello A, Zhu W, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Takagi Y, Richards N.


Reviewed by: Wankowicz S, Fraser JS. - July 2023


Figure from Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase

Peer Review


The mineralocorticoid receptor forms higher order oligomers upon DNA binding

Fettweis G, Johnson TA, Almeida-Prieto B, Presman DM, Hager GL, Alvarez de la Rosa D.


Reviewed by: Wankowicz S, Bergmann L, Fraser JS. - June 2023


Figure from The mineralocorticoid receptor forms higher order oligomers upon DNA binding

Peer Review


Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening

Ma W, Zhang W, Le Y, Shi X, Xu Q, Xiao Y, Dou Y, Wang X, Zhou W, Peng W, Zhang H, Huang B.


Reviewed by: San Felipe CJ, Yamamura H, Fraser J. - June 2023


Figure from Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening

Peer Review


Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks

Johnson SR, Fu X, Viknander S, Goldin C, Monaco S, Zelezniak A, Yang KK.


Reviewed by: Beazer J, Fraser JS. - May 2023


Figure from Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks

Peer Review

Post-Review

Highlight

  • Assessing the laboratory performance of AI-generated enzymes
    • Nature Biotechnology. 2023.
  • Full Text

The conserved protein CBA1 is required for vitamin B12 uptake in different algal lineages

Sayer AP, Llavero-Pasquina M, Geisler K, Holzer A, Bunbury F, Mendoza-Ochoa GI, Lawrence AD, Warren MJ, Mehrshahi P, Smith AG.


Reviewed by: Student 1, Student 2, Macdonald CB, Fraser J. - May 2023


Figure from The conserved protein CBA1 is required for vitamin B12 uptake in different algal lineages

Peer Review


Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity

Yang D, Wang Y, Qi T, Zhang X, Shen L, Ma J, Pang Z, Lal NK, McClatchy DB, Wang K, Xie Y, Polli F, Maximov A, Augustine V, Cline HT, Yates JR III, Ye L.


Reviewed by: Liu Z, and Shin C, Macdonald CB, Fraser J. - May 2023


Figure from Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity

Peer Review


The Herbicide Acetochlor Causes Lipid Peroxidation by Inhibition of Glutathione Peroxidase 4

Mesmar F, Muhsen M, Tourigny JP, Tennessen JM, Bondesson M.


Reviewed by: Byun D, Zheng J, Macdonald CB, Fraser J. - May 2023


Figure from The Herbicide Acetochlor Causes Lipid Peroxidation by Inhibition of Glutathione Peroxidase 4

Peer Review


Decoding the Cure-all Effects of Ginseng

Loo S, Kam A, Dutta B, Zhang X, Feng N, Sze SK, Liu CF, Wang X, Tam JP.


Reviewed by: Chavez I, Rodea D, Ravikumar A, Macdonald CB, Fraser J. - May 2023


Figure from Decoding the Cure-all Effects of Ginseng

Peer Review


Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network

Do, H and Miao, Y.


Reviewed by: Alkislar I, Freitas N, Macdonald CB, Fraser J. - May 2023


Figure from Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network

Peer Review


Quantification of gallium cryo-FIB milling damage in biological lamella

Lucas BA, Grigorieff N.


Reviewed by: Raskar T, Chen D, Fraser JS. - May 2023


Figure from Quantification of gallium cryo-FIB milling damage in biological lamella

Peer Review

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An amino domino model described by a cross peptide bond Ramachandran plot defines amino acid pairs as local structural units

Rosenberg AA, Yehishalom N, Marx A, Bronstein A.


Reviewed by: Ravikumar A, Fraser JS. - April 2023


Figure from An amino domino model described by a cross peptide bond Ramachandran plot defines amino acid pairs as local structural units

Peer Review


Mutation in glutamate transporter homologue GltTk provides insights into pathologic mechanism of episodic ataxia 6

Colucci E, Anshari ZR, Patiño-Ruiz MF, Nemchinova M, Whittaker J, Slotboom DJ, Guskov A.


Reviewed by: Macdonald CB. - March 2023


Figure from Mutation in glutamate transporter homologue GltTk provides insights into pathologic mechanism of episodic ataxia 6

Peer Review


A conserved local structural motif controls the kinetics of PTP1B catalysis

Yeh CY, Izaguirre JA, Greisman JB, Willmore L, Maragakis P, Shaw DE.


Reviewed by: San Felipe CJ, Fraser J. - March 2023


Figure from A conserved local structural motif controls the kinetics of PTP1B catalysis

Peer Review


Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography

Greisman JB, Willmore L, Yeh CY, Giordanetto F, Shahamadtar S, Nisonoff H, Maragakis P, Shaw DE.


Reviewed by: San Felipe CJ, Fraser J. - March 2023


Figure from Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography

Peer Review


Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

Garcia AK, Harris DF, Rivier AJ, Carruthers BM, Pinochet-Barros A, Seefeldt L, Kaçar B.


Reviewed by: Macdonald CB, Lee S. - February 2023


Figure from Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

Peer Review


The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins

Miller AN, Houlihan PR, Matamala E, Cabezas-Bratesco D, Lee GY, Cristofori-Armstrong B, Dilan T, Sanchez-Martinez S, Matthies D, Yan R, Yu Z, Ren D, Brauchi SE, and Clapham DE.


Reviewed by: Anonymous Reviewer, Fraser JS. - February 2023


Figure from The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins

Peer Review

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Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

Mehlman TS, Biel JT, Azeem SM, Nelson ER, Hossain S, Dunnett LE, Paterson NG, Douangamath A, Talon R, Axford D, Orins H, von Delft F, Keedy DA.


Reviewed by: San Felipe CJ, Asthana P, Fraser J. - February 2023


Figure from Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

Peer Review


Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility

Spreacker PJ, Thomas N, Beeninga WF, Brousseau M, Porter CJ, Hibbs KM, Henzler-Wildman KA.


Reviewed by: Macdonald CB. - November 2022


Figure from Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility

Peer Review


Torsion angles to map and visualize the conformational space of a protein

Ginn HM.


Reviewed by: Ravikumar A, Fraser JS. - October 2022


Figure from Torsion angles to map and visualize the conformational space of a protein

Peer Review


Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution

Buda K, Miton CM, Tokuriki N.


Reviewed by: Macdonald CB, Lee S, Fraser JS. - September 2022


Figure from Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution

Peer Review


Cryo-EM structure and B-factor refinement with ensemble representation

Cragnolini T, Beton J, Topf M.


Reviewed by: Wankowicz S, Fraser JS. - August 2022


Figure from Cryo-EM structure and B-factor refinement with ensemble representation

Peer Review


Hydrogens and hydrogen-bond networks in macromolecular MicroED data

Clabbers MTB, Martynowycz MW, Hattne J, Gonen T.


Reviewed by: Asthana P, Fraser JS. - August 2022


Figure from Hydrogens and hydrogen-bond networks in macromolecular MicroED data

Peer Review


The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation

Jabłońska J, Chun-Chen Y, Longo LM, Tawfik DS, Gruic-Sovulj I.


Reviewed by: Ravikumar A, Fraser JS. - July 2022


Figure from The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation

Peer Review


Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

Flynn JM, Samant N, Schneider-Nachum G, Barkan DT, Yilmaz NK, Schiffer CA, Moquin SA, Dovala D, Bolon DNA.


Reviewed by: Macdonald CB, Fraser JS. - June 2022


Figure from Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

Peer Review


Ab initio phasing macromolecular structures using electron-counted MicroED data

Martynowycz MW, Clabbers MTB, Hattne J, and Gonen T.


Reviewed by: Young ID, Fraser JS. - May 2022


Figure from Ab initio phasing macromolecular structures using electron-counted MicroED data

Peer Review


Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin

Ren Z.


Reviewed by: Wolff A, Ravikumar A, Fraser JS. - March 2022


Figure from Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin

Peer Review


Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions

Langstein-Skora I, Schmid A, Emenecker RJ, Richardson MOG, Götz MJ, Payer SK, Korber P, Holehouse AS.


Reviewed by: Chen D, San Felipe CJ, Fraser JS. - March 2022


Figure from Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions

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Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces

Lubin JH, Markosian C, Balamurugan D, Pasqualini R, Arap W, Burley SK, and Khare SD.


Reviewed by: Díaz RE, Fraser JS. - February 2022


Figure from Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces

Peer Review


Single-sequence protein structure prediction using language models from deep learning

Chowdhury R, Bouatta N, Biswas S, Rochereau C, Church GM, Sorger PK, and AlQuraishi M.


Reviewed by: Madani A, Fraser JS. - February 2022


Figure from Single-sequence protein structure prediction using language models from deep learning

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Post-Review

Highlight

  • News & Views: A language model beats alphafold2 on orphans
    • Michaud JM, Madani A, Fraser JS. Nature Biotechnology. 2022.
  • Full Text

Effects of cryo-EM cooling on structural ensembles

Bock LV, and Grubmüller H.


Reviewed by: Young ID, Fraser JS. - October 2021


Figure from Effects of cryo-EM cooling on structural ensembles

Peer Review


Inferring a Continuous Distribution of Atom Coordinates from Cryo-EM Images using VAEs

Rosenbaum D, Garnelo M, Zielinski M, Beattie C, Clancy E, Huber A, Kohli P, Senior AW, Jumper J, Doersch C, Eslami SMA, Ronneberger O, and Adler J.


Reviewed by: Wankowicz SA, Young ID, Asarnow D, Fraser JS. - September 2021


Figure from Inferring a Continuous Distribution of Atom Coordinates from Cryo-EM Images using VAEs

Peer Review


reciprocalspaceship: a Python library for crystallographic data analysis

Greisman JB, Dalton KM, and Hekstra DR.


Reviewed by: Young ID. - September 2021


Figure from reciprocalspaceship: a Python library for crystallographic data analysis

Peer Review


Influenza A M2 Channel Oligomerization is Sensitive to its Chemical Environment

Townsend JA, Sanders HM, Rolland AD, Prell JS, Wang J, and Marty MT.


Reviewed by: Fraser JS, Anonymous Reviewer #1, Anonymous Reviewer #2, Anonymous Reviewer #3, Anonymous Reviewer #4. - June 2021


Figure from Influenza A M2 Channel Oligomerization is Sensitive to its Chemical Environment

Peer Review


Opening of a Cryptic Pocket in β-lactamase Increases Penicillinase Activity

Knoverek CR, Mallimadugula UL, Singh S, Rennella E, Frederick TE, Yuwen T, Raavicharla S, Kay LE, and Bowman GR.


Reviewed by: Coyote-Maestas W, Díaz RE, Fraser JS. - May 2021


Figure from Opening of a Cryptic Pocket in β-lactamase Increases Penicillinase Activity

Peer Review


Mapping the Functional Landscape of the Receptor Binding Domain of T7 Bacteriophage by Deep Mutational Scanning

Huss P, Meger A, Leander M, Nishikawa K, and Raman S.


Reviewed by: Coyote-Maestas W, Fraser JS. - April 2021


Figure from Mapping the Functional Landscape of the Receptor Binding Domain of T7 Bacteriophage by Deep Mutational Scanning

Peer Review

Post-Review

Highlight

  • Virus Engineering: ORACLE reveals a bright future to fight bacteria
    • Coyote-Maestas W, Fraser JS. eLife. 2021.
  • Full Text

Improving SARS-CoV-2 structures: Peer review by early coordinate release

Croll TI, Williams CJ, Chen VB, Richardson DC, and Richardson JS.


Reviewed by: Young ID, Fraser JS. - April 2021


Figure from Improving SARS-CoV-2 structures: Peer review by early coordinate release

Peer Review

Post-Review

Highlight

  • Amenders Assemble!
    • Young ID, Fraser JS. 2021.
  • Zenodo Record: 4678069
  • Full Text

Inhibitor Binding Modulates Protonation States in the Active Site of SARS-CoV-2 Main Protease

Kneller DW, Phillips G, Weiss KL, Zhang Q, Coates L, and Kovalevsky A.


Reviewed by: Correy G, Fraser JS. - January 2021


Figure from Inhibitor Binding Modulates Protonation States in the Active Site of SARS-CoV-2 Main Protease

Peer Review


DNA mismatches reveal conformational penalties in protein–DNA recognition

Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, and Gordân R.


Reviewed by: Kundert K, Fraser JS. - October 2020


Figure from DNA mismatches reveal conformational penalties in protein–DNA recognition

Peer Review

Post-Review

Highlight

  • News & Views: DNA-binding proteins meet their mismatch
    • Kundert K, Fraser JS. Nature. 2020.
  • Full Text

Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes

Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, and Shifman JM.


Reviewed by: Estevam G, Fraser JS. - October 2020


Figure from Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes

Peer Review


Making the invisible enemy visible

Croll T, Diederichs K, Fischer F, Fyfe C, Gao Y, Horrell S, Joseph AP, Kandler L, Kippes O, Kirsten F, Müller K, Nolte K, Payne A, Reeves MG, Richardson J, Santoni G, Stäb S, Tronrud D, Williams C, and Thorn A.


Reviewed by: Young ID, Fraser JS. - October 2020


Figure from Making the invisible enemy visible

Peer Review


The genotype-phenotype landscape of an allosteric protein

Tack DS, Tonner PD, Pressman A, Olson ND, Levy SF, Romantseva EF, Alperovich N, Vasilyeva O, and Ross D.


Reviewed by: Coyote-Maestas W, Fraser JS. - September 2020


Figure from The genotype-phenotype landscape of an allosteric protein

Peer Review


MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP

Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, and Gonen T.


Reviewed by: Young ID, Fraser JS. - September 2020


Figure from MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP

Peer Review


Resolving Individual-Atom of Protein Complex using Commonly Available 300-kV Cryo-electron Microscopes

Zhang K, Pintilie GD, Li S, Schmid MF, and Chiu W.


Reviewed by: Wankowicz S, Fraser JS. - September 2020


Figure from Resolving Individual-Atom of Protein Complex using Commonly Available 300-kV Cryo-electron Microscopes

Peer Review


Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

Durdagi S, Dağ C, Dogan B, Yigin M, Avsar T, Buyukdag C, Erol I, Ertem B, Calis S, Yildirim G, Orhan MD, Guven O, Aksoydan B, Destan E, Sahin K, Besler SO, Oktay L, Shafiei A, Tolu I, Ayan E, Yuksel B, Peksen AB, Gocenler O, Yucel AD, Can O, Ozabrahamyan S, Olkan A, Erdemoglu E, Aksit F, Tanisali G, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Sierra RG, Snell E, and DeMirci H.


Reviewed by: Correy G, Fraser JS. - September 2020


Figure from Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

Peer Review


Small Glycols Discover Cryptic Pockets on Proteins for Fragment-based Approaches

Bansia H, Mahanta P, Yennawar NH, and Ramakumar S.


Reviewed by: Díaz RE, Fraser JS. - August 2020


Figure from Small Glycols Discover Cryptic Pockets on Proteins for Fragment-based Approaches

Peer Review


Navigating Chemical Space By Interfacing Generative Artificial Intelligence and Molecular Docking

Xu Z, Wauchope O, and Frank AT.


Reviewed by: Fraser JS. - June 2020


Figure from Navigating Chemical Space By Interfacing Generative Artificial Intelligence and Molecular Docking

Peer Review


An RNA dynamic ensemble at atomic resolution

Shi H, Rangadurai A, Assi HA, Roy R, Case DA, Herschlag D, Yesselman JD, and Al-Hashimi HM.


Reviewed by: Fraser JS. - May 2020


Figure from An RNA dynamic ensemble at atomic resolution

Peer Review


Using a fragment-based approach to identify novel chemical scaffolds targeting the dihydrofolate reductase (DHFR) from Mycobacterium tuberculosis

Ribeiro JA, Hammer A, Zúñiga GAL, Chavez-Pacheco SM, Tyrakis P, de Oliveira GS, Kirkman T, Bakali JE, Rocco SA, Sforça ML, Parise-Filho R, Coyne AG, Blundell TL, Abell C, and Dias MVB.


Reviewed by: Díaz RE, Chaires HA, Fraser JS. - April 2020


Figure from Using a fragment-based approach to identify novel chemical scaffolds targeting the dihydrofolate reductase (DHFR) from Mycobacterium tuberculosis

Peer Review


Improvement of cryo-EM maps by density modification

Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, and Afonine PV.


Reviewed by: Young ID, Rohou A, Fraser JS. - March 2020


Figure from Improvement of cryo-EM maps by density modification

Peer Review


Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation

Leander M, Yuan Y, Meger A, Cui Q, and Raman S.


Reviewed by: Coyote-Maestas W, Fraser JS. - February 2020


Figure from Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation

Peer Review


Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments

Cruz MA, Frederick TE, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, and Bowman GR.


Reviewed by: Pellegrino J, Fraser JS. - February 2020


Figure from Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments

Peer Review


Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning

Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, and Kosuri S.


Reviewed by: Estevam G, Fraser JS. - January 2020


Figure from Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning

Peer Review


Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution

Bouvier G, Bardiaux B, Pellarin R, Rapisarda C, and Nilges M.


Reviewed by: Díaz RE, Young ID, Fraser JS. - January 2020


Figure from Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution

Peer Review


Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Meisburger SP, Case DA, and Ando N.


Reviewed by: Wolff A, Fraser JS. - October 2019


Figure from Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Peer Review


Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, and Adams PD.


Reviewed by: Wankowicz S, Pierce L, Fraser JS. - August 2019


Figure from Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Peer Review


Measurement of Atom Resolvability in CryoEM Maps with Q-scores

Pintilie G, Zhang K, Su Z, Li S, Schmid MF, and Chiu W.


Reviewed by: Barad B, Fraser JS. - August 2019


Figure from Measurement of Atom Resolvability in CryoEM Maps with Q-scores

Peer Review


Stimulus-responsive self-assembly of protein-based fractals by computational design

Hernández NE, Hansen WA, Zhu D, Shea ME, Khalid M, Manichev V, Putnins M, Chen M, Dodge AG, Yang L, Marrero-Berríos I, Banal M, Rechani P, Gustafsson T, Feldman LC, Lee SH, Wackett LP, Dai W, and Khare SD.


Reviewed by: Young ID, Fraser JS. - June 2019


Figure from Stimulus-responsive self-assembly of protein-based fractals by computational design

Peer Review

Post-Review

Highlight

  • News & Views: Biomaterials in non-integer dimensions
    • Young ID, Fraser JS. Nature Chemistry. 2019.
  • Full Text

A microtubule RELION-based pipeline for cryo-EM image processing

Cook AD, Manka SW, Wang S, Moores CA, and Atherton J.


Reviewed by: Young ID, Fraser JS. - June 2019


Figure from A microtubule RELION-based pipeline for cryo-EM image processing

Peer Review


Identifying dynamic, partially occupied residues using anomalous scattering

Rocchio S, Duman R, Omari KE, Mykhaylyk V, Yan Z, Wagner A, Bardwell JCA, and Horowitz S.


Reviewed by: Correy G, Fraser JS. - May 2019


Figure from Identifying dynamic, partially occupied residues using anomalous scattering

Peer Review


A chemical interpretation of protein electron density maps in the worldwide protein data bank

Yao S, and Moseley HNB.


Reviewed by: Díaz RE, Fraser JS. - April 2019


Figure from A chemical interpretation of protein electron density maps in the worldwide protein data bank

Peer Review


Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis

Verma K, Saxena K, Donaka R, Chaphalkar A, Rai MK, Shukla A, Zaidi Z, Dandage R, Shanmugam D, and Chakraborty K.


Reviewed by: Thompson E, Fraser JS. - February 2019


Figure from Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis

Peer Review


Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size

Martynowycz MW, Zhao W, Hattne J, Jensen GJ, and Gonen T.


Reviewed by: Fraser JS. - September 2018


Figure from Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size

Peer Review


RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix

Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, and Das R.


Reviewed by: Fraser JS. - June 2018


Figure from RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix

Peer Review


Accelerating Scientific Publication in Biology

Vale R.


Reviewed by: Fraser JS. - July 2015


Figure from Accelerating Scientific Publication in Biology

Peer Review