Peer Review
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).
Generative design of novel bacteriophages with genome language models
Samuel H. King, Claudia L. Driscoll, David B. Lii, Daniel Guo, Aditi T. Merchant, Garyk Brixi, Max E. Wilkinson, Brian L. Hie.
Reviewed by: Fraser JS, Bondy-Denomy J. - September 2025
The authors use the Evo series of genomic language models to generate novel phage genomes.
AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network
Alisia Fadini, Minhuan Li, Airlie J. McCoy, Thomas C. Terwilliger, Randy J. Read, Doeke Hekstra, Mohammed AlQuraishi.
Reviewed by: Fraser JS, Wankowicz SA, Chrispens KM. - July 2025
The authors present ROCKET, a method to improve structures from AlphaFold 2 with experimental data from X-ray crystallography, cryoEM, and cryoET.
Conserved energetic changes drive function in an ancient protein fold
Malcolm L. Wells, Chenlin Lu, Daniel Sultanov, Kyle C. Weber, Zhen Gong, Anum Glasgow.
Reviewed by: Kim G, Rao J, Fraser JS, Anonymous Student. - July 2025
This paper explores the energetic relationships of functional specificity in the LacI/GalR family of transcription factors (TFs) and periplasmic binding proteins (PBPs), which share the Venus flytrap fold (VFT) but perform different biological roles.
Have protein-ligand co-folding methods moved beyond memorisation?
Peter Škrinjar, Jérôme Eberhardt, Janani Durairaj, Torsten Schwede.
Reviewed by: Chrispens KM, Hazelwood I, Fraser JS. - June 2025
This paper assesses the performance of recent docking/co-folding methods through a series of stringent tests.
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
Saro Passaro*, Gabriele Corso*, Jeremy Wohlwend*, Mateo Reveiz*, Stephan Thaler*, Vignesh Ram Somnath, Noah Getz, Tally Portnoi, Julien Roy, Hannes Stark, David Kwabi-Addo, Dominique Beaini, Tommi Jaakkola, Regina Barzilay.
Reviewed by: Chrispens KM, Wankowicz SA, Fraser JS. - June 2025
Boltz-2 presents a major update to the Boltz-1 structure prediction model, improves performance, and introduces a new affinity prediction module.
Oligomerization enables the selective targeting of intrinisically disordered regions by small molecules
Stasė Bielskutė, Borja Mateos, Muhammad Awawdy, Carla Garcia-Cabau, Henri Niskanen, Carolina Sánchez-Zarzalejo, Lorenzo Bracaglia, Roberta Pierattelli, Isabella C. Felli, Marta Frigolé-Vivas, Jesús García, Antoni Riera, Denes Hnisz, Xavier Salvatellay.
Reviewed by: Gupta NG, Fraser JS, Coyote-Maestas W, Anonymous Student. - June 2025
Energetic and structural control of polyspecificity in a multidrug transporter
Silas T. Miller, Katherine A. Henzler-Wildman, Srivatsan Raman.
Reviewed by: Hazelwood I, Fraser JS, Coyote-Maestas W, Anonymous Student. - May 2025
This paper analyzes the role of each residue in exporter efficiency by comparing exporter function in different pH conditions, which provide different proton gradients to drive transport.
InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
Simon E, Zou J.
Reviewed by: Chrispens KM, Fraser JS. - January 2025
InterPLM seeks to apply the recently developed techniques for mechanistic interpretability of large language models to protein language models, namely ESM-2.
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
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
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
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
Effects of residue substitutions on the cellular abundance of proteins
Schulze TK, Lindorff-Larsen K.
Reviewed by: Zou Z, Fraser JS. - October 2024
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
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
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
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
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
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
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
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
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
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
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
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
Heterogeneous folding landscapes and predetermined breaking points within a protein family
Pechmann S.
Reviewed by: Macdonald CB and San Felipe CJ. - April 2024
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
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
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
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
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
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
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
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
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
MatchMaps: Non-isomorphous difference maps for X-ray crystallography
Brookner DE, Hekstra DR.
Reviewed by: Asthana P, Correy GJ, Fraser JS. - November 2023
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
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
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
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
- Biorxiv Preprint: 550545
- PREreview.org: 8235543
- Link: https://github.com/GMdSilva/10.5281-zenodo-8235542_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
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
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
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
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
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
- Biorxiv Preprint: 532494
- PREreview.org: doi-10.1101-2023.03.13.532494
Peer Review
- PMID: 38266644
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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
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
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
Quantification of gallium cryo-FIB milling damage in biological lamella
Lucas BA, Grigorieff N.
Reviewed by: Raskar T, Chen D, Fraser JS. - May 2023
- Biorxiv Preprint: 526705
- Review: 2u852i1
- Response: 2ub8gsu
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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
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
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
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
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
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
- Biorxiv Preprint: 506428
- Review: 2t15ojf
- Explanatory tweetstorm by James Fraser
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- PMID: 36695574
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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
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
- Biorxiv Preprint: 471113
- PREreview.org: doi-10.1101-2021.12.04.471113
Peer Review
Torsion angles to map and visualize the conformational space of a protein
Ginn HM.
Reviewed by: Ravikumar A, Fraser JS. - October 2022
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
- Biorxiv Preprint: 505194
- PREreview.org: doi-10.1101-2022.09.07.505194
Peer Review
- PMID: 38129396
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Cryo-EM structure and B-factor refinement with ensemble representation
Cragnolini T, Beton J, Topf M.
Reviewed by: Wankowicz S, Fraser JS. - August 2022
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
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
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
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
Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin
Ren Z.
Reviewed by: Wolff A, Ravikumar A, Fraser JS. - March 2022
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
- Biorxiv Preprint: 480018
- Review: 2pdi1es
- Link: Response to review
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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
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
Effects of cryo-EM cooling on structural ensembles
Bock LV, and Grubmüller H.
Reviewed by: Young ID, Fraser JS. - October 2021
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
reciprocalspaceship: a Python library for crystallographic data analysis
Greisman JB, Dalton KM, and Hekstra DR.
Reviewed by: Young ID. - September 2021
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
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
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
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
Croll and coworkers describe a unique form of peer-review enabled by the early release of biomolecular structure coordinates and density maps and detail its critical role in the search for SARS-CoV-2 vaccines and treatments.
- Zenodo Record: 4697901
Peer Review
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
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
- Biorxiv Preprint: 705558
Peer Review
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
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
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
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
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
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
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
Navigating Chemical Space By Interfacing Generative Artificial Intelligence and Molecular Docking
Xu Z, Wauchope O, and Frank AT.
Reviewed by: Fraser JS. - June 2020
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Accelerating Scientific Publication in Biology
Vale R.
Reviewed by: Fraser JS. - July 2015
