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.

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Mapping the Functional Landscape of the Receptor Binding Domain of T7 Bacteriophage by Deep Mutational Scanning.
Huss P, Meger A, Leander M, Nishikawa K, Raman S.

Reviewed by: Coyote-Maestas W, Fraser JS.

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  • PMID: 33087930
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  • Virus Engineering: ORACLE reveals a bright future to fight bacteria.
  • Coyote-Maestas W, Fraser JS.. eLife. 2021.
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Improving SARS-CoV-2 structures: Peer review by early coordinate release.
Croll TI, Williams CJ, Chen VB, Richardson DC, Richardson JS.

Reviewed by: Young ID, Fraser JS.

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.
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  • Zenodo Record: 4697901


Reciprocalspaceship: A Python Library for Crystallographic Data Analysis
Greisman JB, Dalton KM, Hekstra DR.

Reviewed by: Young ID.

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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, Kovalevsky A.

Reviewed by: Correy G, Fraser JS.

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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, Gordân R.

Reviewed by: Kundert K, Fraser JS.

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    Peer Review
  • Biorxiv Preprint v1: 705558
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  • PMID: 33087930
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  • News & Views: DNA-binding proteins meet their mismatch.
  • Kundert K, Fraser JS. Nature. 2020.
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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, Shifman JM.

Reviewed by: Estevam G, Fraser JS.

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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, Thorn A.

Reviewed by: Young ID, Fraser JS.

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The genotype-phenotype landscape of an allosteric protein.
Tack DS, Tonner PD, Pressman A, Olson ND, Levy SF, Romantseva EF, Alperovich N, Vasilyeva O, Ross D.

Reviewed by: Coyote-Maestas W, Fraser JS.

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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, Gonen T.

Reviewed by: Young ID, Fraser JS.

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Resolving Individual-Atom of Protein Complex using Commonly Available 300-kV Cryo-electron Microscopes.
Zhang K, Pintilie GD, Li S, Schmid MF, Chiu W.

Reviewed by: Wankowicz S, Fraser JS.

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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, Dag 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, DeMirci H.

Reviewed by: Correy G, Fraser JS.

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Small Glycols Discover Cryptic Pockets on Proteins for Fragment-based Approaches.
Bansia H, Mahanta P, Yennawar NH, Ramakumar S.

Reviewed by: Díaz RE, Fraser JS.

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Navigating Chemical Space By Interfacing Generative Artificial Intelligence and Molecular Docking.
Xu Z, Wauchope O, Frank AT.

Reviewed by: Fraser JS.

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An RNA dynamic ensemble at atomic resolution.
Shi H, Rangadurai A, Assi HA, Roy R, Case DA, Herschlag D, Yesselman JD, Al-Hashimi HM.

Reviewed by: Fraser JS.

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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, Dias MVB.

Reviewed by: Díaz RE, Chaires HA, Fraser JS.

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Improvement of cryo-EM maps by density modification.
Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, Afonine PV.

Reviewed by: Young ID, Rohou A, Fraser JS.

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Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation.
Leander M, Yuan Y, Meger A, Cui Q, Raman S.

Reviewed by: Coyote-Maestas W, Fraser JS.

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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, Bowman GR.

Reviewed by: Pellegrino J, Fraser JS.

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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, Kosuri S.

Reviewed by: Estevam G, Fraser JS.

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Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution.
Bouvier G, Bardiaux B, Pellarin R, Rapisarda C, Nilges M.

Reviewed by: Díaz RE, Young ID, Fraser JS.

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Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal.
Meisburger SP, Case DA, Ando N.

Reviewed by: Wolff A, Fraser JS.

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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, Adams PD.

Reviewed by: Wankowicz S, Pierce L, Fraser JS.

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Measurement of Atom Resolvability in CryoEM Maps with Q-scores.
Pintilie G, Zhang K, Su Z, Li S, Schmid MF, Chiu W.

Reviewed by: Barad B, Fraser JS.

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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, Khare SD.

Reviewed by: Young ID, Fraser JS.

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  • PMID: 31209296
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  • News & Views: Biomaterials in non-integer dimensions.
  • Young ID, Fraser JS. Nature Chemistry. 2019.
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A microtubule RELION-based pipeline for cryo-EM image processing.
Cook AD, Manka SW, Wang S, Moores CA, Atherton J.

Reviewed by: Young ID, Fraser JS.

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Identifying dynamic, partially occupied residues using anomalous scattering.
Rocchio S, Duman R, Omari KE, Mykhaylyk V, Yan Z, Wagner A, Bardwell JCA, Horowitz S.

Reviewed by: Correy G, Fraser JS.

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A chemical interpretation of protein electron density maps in the worldwide protein data bank.
Yao S, Moseley HNB.

Reviewed by: Díaz RE, Fraser JS.

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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, Chakraborty K.

Reviewed by: Thompson E, Fraser JS.

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Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size.
Martynowycz MW, Zhao W, Hattne J, Jensen GJ, Gonen T.

Reviewed by: Fraser JS.

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RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix.
Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R.

Reviewed by: Fraser JS.

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Accelerating Scientific Publication in Biology.
Vale R.

Reviewed by: Fraser JS.

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