PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction

Attention Is All You Need

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Highly accurate protein structure prediction with AlphaFold

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Untitled work

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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

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The MARTINI Coarse-Grained Force Field: Extension to Proteins

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Martini 3: A general purpose force field for coarse-grained molecular dynamics

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DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networksPreprint

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HELIQUEST: a web server to screen sequences with specific α-helical properties

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Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.

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The helical hydrophobic moment: a measure of the amphiphilicity of a helix

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Curvature of clathrin-coated pits driven by epsin

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Describing the Mechanism of Antimicrobial Peptide Action with the Interfacial Activity Model

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Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway

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A general amphipathic α-helical motif for sensing membrane curvature

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Amphipathic helices and membrane curvature

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Role of the ENTH Domain in Phosphatidylinositol-4,5-Bisphosphate Binding and Endocytosis

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ArfGAP1 responds to membrane curvature through the folding of a lipid packing sensor motif

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3Dmol.js: molecular visualization with WebGL

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Spatial arrangement of proteins in planar and curved membranes by PPM 3.0

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The ARF1 GTPase-Activating Protein: Zinc Finger Motif and Golgi Complex Localization

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Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer curvature

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When Physics Takes Over: BAR Proteins and Membrane Curvature

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Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L)

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Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins

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modlAMP: Python for antimicrobial peptides

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α-Synuclein and ALPS motifs are membrane curvature sensors whose contrasting chemistry mediates selective vesicle binding

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A phosphorylation-regulated amphipathic helix controls the membrane translocation and function of the yeast phosphatidate phosphatase

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Contrasting Membrane Interaction Mechanisms of AP180 N-terminal Homology (ANTH) and Epsin N-terminal Homology (ENTH) Domains

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Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation

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Structural basis of carotenoid cleavage: From bacteria to mammals

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Membrane Curvature Sensing by Amphipathic Helices

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Requirements for the mitochondrial import and localization of dihydroorotate dehydrogenase

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Two Lipid-Packing Sensor Motifs Contribute to the Sensitivity of ArfGAP1 to Membrane Curvature

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The interactions of peripheral membrane proteins with biological membranes

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Curvature Sensing by the Epsin N-Terminal Homology Domain Measured on Cylindrical Lipid Membrane Tethers

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Solution Structure and Lipid Membrane Partitioning of VSTx1, an Inhibitor of the KvAP Potassium Channel,

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Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus

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TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures

Dobson, L., Szekeres, L. I., Gerdán, C., Langó, T., Zeke, A., & Tusnády, G. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac928 · Cited by 87 · see citing works

The α-Helical Domain of Liver Fatty Acid Binding Protein Is Responsible for the Diffusion-Mediated Transfer of Fatty Acids to Phospholipid Membranes

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Mutation of Tryptophan Residues in Lipoprotein Lipase

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Localization and targeting of the VP14 epoxy‐carotenoid dioxygenase to chloroplast membranes

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Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis

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Structural insights into the cooperative remodeling of membranes by amphiphysin/BIN1

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Role of Helix 0 of the N-BAR Domain in Membrane Curvature Generation

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Peripheral membrane proteins: Tying the knot between experiment and computation

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Mechanism of human PTEN localization revealed by heterologous expression in Dictyostelium

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Membrane binding motif of the P-type cardiotoxin

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Structural Basis for the Golgi Association by the Pleckstrin Homology Domain of the Ceramide Trafficking Protein (CERT)

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STARD4 Membrane Interactions and Sterol Binding

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Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain

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High-Level Expression and Mutagenesis of Recombinant Human Phosphatidylcholine Transfer Protein Using a Synthetic Gene: Evidence for a C-Terminal Membrane Binding Domain

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Structure and Dynamics of Helix-0 of the N-BAR Domain in Lipid Micelles and Bilayers

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An Experiment-Based Algorithm for Predicting the Partitioning of Unfolded Peptides into Phosphatidylcholine Bilayer Interfaces

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Discovery of novel membrane binding structures and functions

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Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders

van Hilten, N., Methorst, J., Verwei, N., & Risselada, H. J. (2023) · Science Advances · doi:10.1126/sciadv.ade8839 · Cited by 49 · see citing works

Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels

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Protein-Membrane Interaction and Fatty Acid Transfer from Intestinal Fatty Acid-binding Protein to Membranes

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Specific and Nonspecific Membrane-binding Determinants Cooperate in Targeting Phosphatidylinositol Transfer Protein β-Isoform to the MammalianTrans-Golgi Network

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Membrane Topology of Helix 0 of the Epsin N-terminal Homology Domain

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Envelope-deforming antiviral peptide derived from influenza virus M2 protein

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Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36

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Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning

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Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

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Dissecting peripheral protein-membrane interfaces

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Use of the Parallax-Quench Method to Determine the Position of the Active-Site Loop of Cholesterol Oxidase in Lipid Bilayers

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A Highly Active, Soluble Mutant of the Membrane-Associated (S)-Mandelate Dehydrogenase from Pseudomonas putida

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Monitoring glycolipid transfer protein activity and membrane interaction with the surface plasmon resonance technique

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Structural basis for the inhibition of voltage-dependent K+ channel by gating modifier toxin

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DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design

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Glycolipid transfer protein: Clear structure and activity, but enigmatic function

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Membrane binding of the insertion sequence of Proteus vulgaris L-amino acid deaminase stabilizes protein structure and increases catalytic activity

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The role of human monoacylglycerol lipase (hMAGL) binding pocket in breakup of unsaturated phospholipid membranes

Karageorgos, I. L., Silin, V. I., Zvonok, N., Marino, J. P., Janero, D. R., & Makriyannis, A. (2017) · Analytical Biochemistry · doi:10.1016/j.ab.2017.08.009 · Cited by 3 · see citing works

Lipase-mediated selective hydrolysis of lipid droplets in phase separated-liposomesPreprint

Papadopoulou, P., van der Pol, R., van Hilten, N., Moradi, M., Ferraz, M. J., Aerts, J. M. F. G., Risselada, H. J., Sevink, A. G. J., & Kros, A. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-9q9wh · Cited by 1 · see citing works

CLCC1 promotes hepatic neutral lipid flux and nuclear pore complex assembly

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The C-terminal sequences of Bcl-2 family proteins mediate interactions that regulate cell death

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When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases

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Using deep learning and large protein language models to predict protein–membrane interfaces of peripheral membrane proteins

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Recognition and remodeling of endosomal zones by sorting nexins

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MOH: A Novel Multilayer Multi-Omics Heterogeneous Graph for Single-Cell Clustering

Dong, Y., Chen, C., Shi, J., Hu, Y., Cao, X., Dong, Y., & Zhang, X. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3589464 · Cited by 7 · see citing works

Tracking Disordered Extracellular Domains of Membrane Proteins in the Cell with Cu(II)-Based Spin Labels

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Amphipathic helices sense the inner nuclear membrane environment through lipid packing defectsPreprint

Lee, S., Roux, A. L., Mors, M., Vanni, S., Roca‐Cusachs, P., & Bahmanyar, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.14.623600 · Cited by 7 · see citing works

SNARE chaperone Sly1 directly mediates close-range vesicle tethering

Duan, M., Plemel, R. L., Takenaka, T., Lin, A., Delgado, B., Nattermann, U., Nickerson, D. P., Mima, J., Miller, E. A., & Merz, A. J. (2024) · The Journal of Cell Biology · doi:10.1083/jcb.202001032 · Cited by 6 · see citing works

The FAM114A proteins are adaptors for the recycling of Golgi enzymes

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Designing a Potent, Low-Toxicity Antimicrobial Peptide Inspired by Scorpion Peptides: Optimizing Expression and Activity

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Host-encoded ETP2 is involved in recruiting the dynamin-like protein ETP9 to the endosymbiont division site in trypanosomatid Angomonas deanei

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Curvature-Sensing Peptides for Virus and Extracellular Vesicle Applications

Lee, C., Jannah, F., Sut, T. N., Haris, M., & Jackman, J. A. (2025) · ACS Nano · doi:10.1021/acsnano.5c08239 · Cited by 3 · see citing works

Unpacking the Tumor Protein D52-like Family: Roles in Intracellular Trafficking and Cancer Progression

Dorward, E. L., Ortiz, M., Weekley, C. M., Min, K. K. M., Duijf, P. H. G., Barreto, S. G., Parker, M. W., & Bonder, C. S. (2026) · Cells · doi:10.3390/cells15030252 · Cited by 3 · see citing works

Decoding Protein–Membrane Binding Interfaces from Surface-Fingerprint-Based Geometric Deep Learning and Molecular Dynamics Simulations

Park, B., & Lehn, R. C. V. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02566 · Cited by 3 · see citing works

AI-driven design of antimicrobial peptide for combating resistance and infectious diseases

Mehraj, I., Dar, T. U. H., Bhat, R. A. H., Hamid, A., Sheikh, W. M., Beigh, A., & Bhat, S. S. (2026) · Pathology - Research and Practice · doi:10.1016/j.prp.2026.156445 · Cited by 3 · see citing works

The role of amphipathic and cationic helical peptides in Parkinson's disease

Pintado‐Grima, C., & Ventura, S. (2024) · Protein Science · doi:10.1002/pro.70020 · Cited by 3 · see citing works

Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape

(2026) · doi:10.1126/science.aea6343 · Cited by 3 · see citing works

Chemical Biology Drives Membrane-Curvature-Sensing Peptide Probes for Extracellular Vesicle Capture and Applications

Sun, G., & Yin, H. H. (2026) · Biochemistry · doi:10.1021/acs.biochem.5c00700 · Cited by 2 · see citing works

A novel fish virus-derived chimeric peptide for intracellular delivery of nucleic acid

Sathiyanarayanan, A., Khangembam, V. C., Pande, A., Pandey, N., Goswami, M., & Thakuria, D. (2025) · Journal of Drug Delivery Science and Technology · doi:10.1016/j.jddst.2025.107327 · Cited by 1 · see citing works

PepMCP: a graph-based membrane contact probability predictor for membrane-lytic antimicrobial peptides

Dong, R., Awang, T., Cao, Q., Kang, K., Wang, L., Zhu, Z., & Song, C. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag453 · Cited by 1 · see citing works

Antibacterial Activity and Action Mechanism of Synthetic Interleukin‐8 Derived Peptides Against Flavobacterium psychrophilum

Santana, P., Tamayo, L., Stambuk, F., Aguilar, L. F., Cortés, M., Guzmán, F., Forero, J. C., Romero, M. S., & Álvarez, C. (2024) · Journal of Fish Diseases · doi:10.1111/jfd.14056 · Cited by 1 · see citing works

Host-derived antimicrobial peptides enhance survival in Vibrio-infected scallop larvae through dual antibacterial and immunomodulatory actions

Revilla, J., Guzmán, F., Cárdenas, C., Oyanedel, D., Araya, M., Álvarez, C., Schmitt, P., & Brokordt, K. (2026) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2026.111488

A novel host-encoded protein, ETP2, plays an important role in endosymbiont division in the trypanosomatid Angomonas deaneiPreprint

Maurya, A. K., Cadena, L. R., Ehret, G., & Nowack, E. C. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.22.649992

Selection inference in a complex genomic landscape: the impact of polymorphic inversionsPreprint

Morales-García, J., Babik, W., Zieliński, P., & Nadachowska‐Brzyska, K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.01.662526

Effects of Δ motY mutations on motility behavior of Pseudomonas aeruginosa chimeric periplasmic stator variantsPreprint

Ferguson, N., Desai, M., Silva, J. F., Nguyen, H., Rodenborn, B., Shindell, O., & Healy, F. G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.06.686970

Lipidomic Profile Reconstruction of Therapeutic Membrane Targets Using Physics‐Based Optimization with Limited Activity Data

Krebs, M., & Risselada, H. J. (2026) · Advanced Science · doi:10.1002/advs.76899 · Cited by 1 · see citing works

A Localization-Based Motif Combination Approach To the Design of Antimicrobial Peptides Targeting Gram-Positive and Gram-Negative Bacteria

Kesmen, Z., Batman, S. G., Canpolat, M., & Büyükkiraz, M. E. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10875-x

SNX-mediated biogenesis of a plant-unique vesicle derived from the multivesicular body

Li, Y., Tao, R., Zhang, H., Wen, X., Leung, S. K. P., Qi, Q., Zheng, X., Guo, H., Wu, C., Fu, Z., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71067-x

Kinase-gated coincidence detection controls kinesin-driven lysosome transportPreprint

O’Regan, L., Bristow, S., Antón, Z., Bodzęta, A., Cross, J. A., Woolfson, D. N., & Dodding, M. P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.27.714776

A narrow thermodynamic design window governs selective membrane permeabilization and antiviral activity of amphipathic peptidesPreprint

van Hilten, N., von Maltitz, P., Aschmann, D., Hoernke, M., Krebs, M., Methorst, J., Kros, A., Münch, J., & Risselada, H. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.20.719566

The Effect of Aza-Glycine Substitution on the Internalization of Dabcyl-Containing Short Oligoarginine

Tarchoun, K., Soltész, D. B., Szabó, I., Song, J., Lee, H., & Bánóczi, Z. (2026) · Biomedicines · doi:10.3390/biomedicines14051025

Expansion of Olfactory Receptor Family 14 Across Fossorial and Insectivorous MammalsPreprint

Ryan, L., & Hughes, G. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.15.738794

MPLID (Membrane Protein–Lipid Interaction Database): A Large-Scale Experimental Resource of Residue-Level Protein–Lipid Contacts

Omage, F. B., & Neshich, G. (2026) · GigaScience · doi:10.1093/gigascience/giag080

Screening of amphipathic helices identifies features linked to inner nuclear membrane properties

Lee, S., Roux, A. L., Goudge, M. C., Mors, M., Vanni, S., Roca‐Cusachs, P., & Bahmanyar, S. (2026) · Nature Communications · doi:10.1038/s41467-026-75561-0

A Comprehensive In-Silico Pipeline for the Discovery of Non-toxic, Stable Antimicrobial Peptides From Databases for Targeting Multi-Drug Resistant K. pneumoniae

Sharma, P., Noman, A. A., Talukder, M. A. A., Parvez, M. J., Hafiz, M. A., Nath, B., & Sharma, H. (2026) · Bioinformatics and Biology Insights · doi:10.1177/11779322261475821

A minimal Asgard archaeal ESCRT-III system remodels membranes across scalesPreprint

Schwille, P., Zivkovic, H., Hrebík, D., Frohn, B. P., Basquin, J., Riggi, M., & Briggs, J. A. G. (2026) · Research Square · doi:10.21203/rs.3.rs-10742307/v1

In silico design and In Vitro validation of WK15: a promising antimicrobial peptide for aquaculture applications

Lohumi, Y., Bhat, R. A. H., Bisht, I., & Pande, A. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05232-1

An artificially developed peptide with anti-oomycete activity against Saprolegnia

Tandel, R. S., Chanu, K. V., Dash, P., Bhat, R. A. H., & Thakuria, D. (2026) · Fisheries Science · doi:10.1007/s12562-026-02021-5

RK-14: A Novel Antimicrobial Peptide Targeting Multidrug-Resistant Bacteria and Catheter-Associated Biofilms

Mehraj, I., Pandit, R. K., Qureshi, S., Ganai, N. A., Dar, T. U. H., Najar, M. A., Shafiq, M., & Bhat, S. S. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-026-11226-0

Reading the Lipid Code: Cooperative Domain Functions in Perilipin Targeting to Lipid Droplets

Stříbný, J., & Schneiter, R. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.113619

Using deep learning and large protein language models to predict protein–membrane interfaces of peripheral membrane proteins

Paranou, D., Chatzigoulas, A., & Cournia, Z. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae078 · Cited by 8 · see citing works

Decoding Protein–Membrane Binding Interfaces from Surface-Fingerprint-Based Geometric Deep Learning and Molecular Dynamics Simulations

Park, B., & Lehn, R. C. V. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02566 · Cited by 3 · see citing works

pLMMoRF: A Web Server That Accurately Predicts Membrane-interacting Molecular Recognition Features by Employing a Protein Language Model

Csepi, M., Berta, B., Basu, S., Kurgan, L., & Hegedűs, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169236 · Cited by 2 · see citing works

Predicting protein-protein binding sites in membrane proteins

Bordner, A. J. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-312 · Cited by 37 · see citing works

Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning

Chatzigoulas, A., & Cournia, Z. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbab518 · Cited by 32 · see citing works