What I Do 2025/2026
Presentation 2025 Sep
Automated model building and protein identification in cryo-EM maps. Jamali K, Käll L, Zhang R, Brown A, Kimanius D, Scheres SHW. Nature. 2024 Nature. Apr 11;628(8007):450–457.
github: ModelAngelo (open-source MIT license)Presentation 2025 Aug
Fast and accurate protein structure search with Foldseek. van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, Söding J, Steinegger M. Nat Biotechnol. 2024 Feb;42(2):243-246.Presentation 2025 Jun
MolViewSpec: a Mol* extension for describing and sharing molecular visualizations. Midlik A, Bittrich S, Fleming JR, Nair S, Velankar S, Burley SK, Young JY, Vallat B, Sehnal D. Nucleic Acids Res. 2025 May 6:gkaf370. Online ahead of print. [website: code, documentation, examples]Presentation 2025 Mar
A structural biology compatible file format for atomic force microscopy. Jiang Y, Wang Z, Scheuring S. Nat Commun. 2025 Feb 15;16(1):1671. [github]Presentation 2025 Feb
Mesoscale explorer: Visual exploration of large-scale molecular models. Rose A, Sehnal D, Goodsell DS, Autin L. Protein Sci. 2024 Oct;33(10):e5177.
https://molstar.org/me/Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0. Chareshneu A, Cantara A, Tichý D, Sehnal D. Curr Protoc. 2024 Dec;4(12):e70070. [github]
https://molstar.org/volumes-and-segmentations/
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Chareshneu A, Midlik A, Ionescu CM, Rose A, Horský V, Cantara A, Svobodová R, Berka K, Sehnal D. Nucleic Acids Res. 2023 May 17:gkad411.Presentation 2024 Oct
Extending cryoDRGN to electron tomography [previous presentation on cryoDRGN]
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Powell BM, Davis JH. Nat Methods. 2024 Aug;21(8):1525-1536. [tomodrgn github]CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Rangan R, Feathers R, Khavnekar S, Lerer A, Johnston JD, Kelley R, Obr M, Kotecha A, Zhong ED. Nat Methods. 2024 Aug;21(8):1537-1545. [cryodrgn github] (version 3.0.0-beta)Presentation 2024 Aug
CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2. Shor B, Schneidman-Duhovny D. Nat Methods. 2024 Mar;21(3):477-487.Presentation 2024 June
Visualizing the residue interaction landscape of proteins by temporal network embedding. Franke L, Peter C. J Chem Theory Comput. 2023 May 23;19(10):2985-2995.Presentation 2024 April
KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities. Guerra JVS, Ribeiro-Filho HV, Pereira JGC, Lopes-de-Oliveira PS. Nucleic Acids Res. 2023 May 4:gkad324. [web server]ParKVFinder: A thread-level parallel approach in biomolecular cavity detection Guerra JVDS et al., SoftwareX. 2020 Jul-Dec;100606.
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science Guerra JVDS, Ribeiro-Filho HV, Jara GE, Bortot LO, Pereira JGC, Lopes-de-Oliveira PS. BMC Bioinformatics. 2021 Dec 20;22(1):607.Presentation 2024 February
AlphaFill: enriching AlphaFold models with ligands and cofactors. Hekkelman ML, de Vries I, Joosten RP, Perrakis A. Nat Methods. 2023 Feb;20(2):205-213. [website] [github]AlphaFold-latest includes modeling nucleic acids, small molecules, and covalent modifications along with proteins
[Oct 2023 press release] [drug discovery angle] [results PDF]Presentation 2023 November
SlicerTMS: Interactive Real-time Visualization of Transcranial Magnetic Stimulation using Augmented Reality and Deep Learning. Franke L, Park TY, Luo J, Rathi Y, Pieper S, Ning L, Haehn D. ArXiv. 2023 May 23:arXiv:2305.06459v3. Preprint.
Open source and data: https://github.com/lorifranke/SlicerTMSPresentation 2023 September
SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality. Pinter C, Lasso A, Choueib S, Asselin M, Fillion-Robin JC, Vimort JB, Martin K, Jolley MA, Fichtinger G. IEEE Trans Med Robot Bionics. 2020 May;2(2):108-117.
www.SlicerVR.org (→ Kitware github)Presentation 2023 July
StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Lugmayr W, Kotov V, Goessweiner-Mohr N, Wald J, DiMaio F, Marlovits TC. Nat Protoc. 2023 Jan;18(1):239-264.Presentation 2023 May
MEinVR: Multimodal Interaction Paradigms in Immersive Exploration. Yuan, ZY; Liu, Y and Yu, LY. 21st IEEE International Symposium on Mixed and Augmented Reality (ISMAR) Adjunct 2022, pp.85-90. [PDF]Presentation 2023 April
AlphaFold predictions: great hypotheses but no match for experiment Terwilliger TC, Liebschner D, [...] Richardson JS, Read RJ, Adams PD. bioRxiv 2022.11.21.517405; doi: https://doi.org/10.1101/2022.11.21.517405Improved AlphaFold modeling with implicit experimental information. Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD. Nat Methods. 2022 Nov;19(11):1376-1382.
(Phenix version of AlphaFold2 Colab: https://github.com/phenix-project/Colabs)Accelerating crystal structure determination with iterative AlphaFold prediction. Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD. Acta Crystallogr D Struct Biol. 2023 Mar 1;79(Pt 3):234-244.
Presentation 2023 February
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction. Tubiana J, Schneidman-Duhovny D, Wolfson HJ. Nat Methods. 2022 Jun;19(6):730-739.
ScanNet: A web server for structure-based prediction of protein binding sites with geometric deep learning. Tubiana J, Schneidman-Duhovny D, Wolfson HJ. J Mol Biol. 2022 Oct 15;434(19):167758.Presentation 2022 October
Protein Cavity/Tunnel Analysis: MOLE, HOLE, HOLLOW, MolAxis...Presentation 2022 September
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Zhong ED, Bepler T, Berger B, Davis JH. Nat Methods. 2021 Feb;18(2):176-185.Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN. Kinman LF, Powell BM, Zhong ED, Berger B, Davis JH. Nat Protoc. 2023 Feb;18(2):319-339. doi: 10.1038/s41596-022-00763-x.
ABCFold: easier running and comparison of AlphaFold 3, Boltz-1, and Chai-1. Elliott, LG; Simpkin, AJ and Rigden, DJ. Bioinformatics Adv. 2025; 5 (1).
source code, instructions, examples available on githubMIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures. Shub L, Liu W, Skiniotis G, Keiser MJ, Robertson MJ. Nat Commun. 2025 Jul 4;16(1):6182.
CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets. Levy A, Raghu R, Feathers JR, Grzadkowski M, Poitevin F, Johnston JD, Vallese F, Clarke OB, Wetzstein G, Zhong ED. Nat Methods. 2025 Jun 26. Online ahead of print.
Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments. Alharbi R, Strnad O, Luidolt LR, Waldner M, Kouril D, Bohak C, Klein T, Groeller E, Viola I. IEEE Trans Vis Comput Graph. 2023 Mar 1;29(3):1860-1875. [PDF]
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Sanchez-Garcia R, Gomez-Blanco J, Cuervo A, Carazo JM, Sorzano COS, Vargas J. Commun Biol. 2021 Jul 15;4(1):874.
Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Tavakoli MR, Lyudchik J, Januszewski M, Vistunou V, Agudelo Dueñas N, Vorlaufer J, Sommer C, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Nature. 2025 Jun 12;642(8067):398-410.
Exploring structural diversity across the protein universe with The Encyclopedia of Domains. Lau AM, Bordin N, Kandathil SM, Sillitoe I, Waman VP, Wells J, Orengo CA, Jones DT. Science. 2024 Nov;386(6721):eadq4946.
TED website: https://ted.cathdb.info/MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts. Philipp M, Moth CW, Ristic N, Tiemann JKS, Seufert F, Panfilova A, Meiler J, Hildebrand PW, Stein A, Wiegreffe D, Staritzbichler R. Nucleic Acids Res. 2024 Jul 5;52(W1):W132-W139.
web server (1-few hours calculation): https://mutationexplorer.vda-group.de/mutation_explorer/submitEspaloma
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Chem Sci. 2024 Aug 14;15(32):12861-12878.Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Nat Methods. 2024 Jun 25. doi: 10.1038/s41592-024-02321-7. Online ahead of print.
AlphaMissense
Accurate proteome-wide missense variant effect prediction with AlphaMissense. Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, Pritzel A, Wong LH, Zielinski M, Sargeant T, Schneider RG, Senior AW, Jumper J, Hassabis D, Kohli P, Avsec Ž. Science. 2023 Sep 22;381(6664):eadg7492.The genetic architecture of protein stability. Faure AJ, Martí-Aranda A, Hidalgo-Carcedo C, Beltran A, Schmiedel JM, Lehner B. Nature. 2024 Oct 24;634(8035):995-1003.
Scalable protein design using optimization in a relaxed sequence space. Frank C, Khoshouei A, Fuβ L, Schiwietz D, Putz D, Weber L, Zhao Z, Hattori M, Feng S, de Stigter Y, Ovchinnikov S, Dietz H. Science. 2024 Oct 25;386(6720):439-445.
AlphaLink: AlphaFold2 modified to incorporate experimental distance restraints
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Stahl K, Graziadei A, Dau T, Brock O, Rappsilber J. Nat Biotechnol. 2023 Dec;41(12):1810-1819. doi: 10.1038/s41587-023-01704-z.MoLPC: larger assemblies from AlphaFold2 dimers and trimers by MC tree search
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search. Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A. Nat Commun. 2022 Oct 12;13(1):6028. doi: 10.1038/s41467-022-33729-4.How accurately can one predict drug binding modes using AlphaFold models? Karelina M, Noh JJ, Dror RO. Elife. 2023 Dec 22;12:RP89386. doi: 10.7554/eLife.89386.
DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model. Lu W, Zhang J, Huang W, Zhang Z, Jia X, Wang Z, Shi L, Li C, Wolynes PG, Zheng S. Nat Commun. 2024 Feb 5;15(1):1071. doi: 10.1038/s41467-024-45461-2.
Demo: https://m1.galixir.com/#/home/demo/dynamicDocking
Web server (requires registration): https://m1.galixir.com/dynamicExternalLink.html#/dynamic-submit
Code: https://github.com/luwei0917/DynamicBindRoseTTAFold and RFdiffusion All-Atom Versions
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Science. 2024 Apr 19;384(6693):eadl2528. doi: 10.1126/science.adl2528.De novo design of protein structure and function with RFdiffusion. Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, Wang J, Venkatesh P, Sappington I, Torres SV, Lauko A, De Bortoli V, Mathieu E, Ovchinnikov S, Barzilay R, Jaakkola TS, DiMaio F, Baek M, Baker D. Nature. 2023 Aug;620(7976):1089-1100. doi: 10.1038/s41586-023-06415-8.
LifeSoaks (included in ProteinsPlus web server)
LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments. Pletzer-Zelgert J, Ehrt C, Fender I, Griewel A, Flachsenberg F, Klebe G, Rarey M. Acta Crystallogr D Struct Biol. 2023 Sep 1;79(Pt 9):837-856.MiCellAnnGELo: annotate microscopy time series of complex cell surfaces with 3D virtual reality. Platt A, Lutton EJ, Offord E, Bretschneider T. Bioinformatics. 2023 Jan 1;39(1):btad013.
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. Lomize AL, Todd SC, Pogozheva ID. Protein Sci. 2022 Jan;31(1):209-220. doi: 10.1002/pro.4219.
PPM Web Server: Positioning of proteins in membraneswebKnossos in-browser annotation tool for very large 3D EM datasets
webKnossos: efficient online 3D data annotation for connectomics. Boergens KM, Berning M, Bocklisch T, Bräunlein D, Drawitsch F, Frohnhofen J, Herold T, Otto P, Rzepka N, Werkmeister T, Werner D, Wiese G, Wissler H, Helmstaedter M. Nat Methods. 2017 Jul;14(7):691-694. Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Yariv B, Yariv E, Kessel A, Masrati G, Chorin AB, Martz E, Mayrose I, Pupko T, Ben-Tal N. Protein Sci. 2023 Mar;32(3):e4582.