Explanipedia

Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability Open

Wei Liu, Jianguo Li, Chandra Verma, Hwee Kuan Lee · 2025

Cyclic peptides are promising drug candidates due to their ability to modulate intracellular protein-protein interactions, a property often inaccessible to small molecules. However, their typically poor membrane permeability limits therape…

A Multiscale Framework for Uncovering Surfactant Mediated Viral Capsid Disruption Open

Srdan Masirevic, Jan K. Marzinek, Muwen Kong, Grace Lin, Hongling Chen , et al. · 2025

Disinfection remains a critical strategy for controlling the transmission of infectious diseases. However, small non-enveloped viruses exhibit exceptional resistance to many disinfectants, often requiring harsh protein-disrupting chemicals…

384 | PROGNOSTIC AND FUNCTIONAL IMPACT OF EGF‐JAK/STAT PATHWAY MUTATIONS IN ANGIOIMMUNOBLASTIC T‐CELL LYMPHOMA Open

David C.S. Huang, Jing Quan Lim, Leonardo Biral, Chee Leong Cheng, Chandra Verma , et al. · 2025

Responsiveness of different MET tumour alterations to type I and type II MET inhibitors Open

Yonina R. Murciano‐Goroff, Valentina Foglizzo, Jason Chang, Natasha Rekhtman, Ann Elizabeth Sisk , et al. · 2025

Background Mutations in c‐MET receptor tyrosine kinase (MET) can be primary oncogenic drivers of multiple tumour types or can be acquired as mechanisms of resistance to therapy. MET tyrosine kinase inhibitors (TKIs) are classified as type …

Conserved leucine-rich repeat proteins in the adhesive projectile slime of velvet worms Open

Zhaolong Hu, Alexander B. Baer, Lars Hering, Ivo de Sena Oliveira, Alexandre Poulhazan , et al. · 2025

The slime of velvet worms (Onychophora) is a protein-based bioadhesive that undergoes rapid, yet reversible transition from a fluid into stiff fibers used for prey capture and defense, but the mechanism by which this phase transition funct…

Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer Open

Dario De Felice, Alessandro Alaimo, Davide Bressan, Sacha Genovesi, Elisa Marmocchi , et al. · 2024

Phase-separating peptide coacervates with programmable material properties for universal intracellular delivery of macromolecules Open

Yue Sun, Xi Wu, Jianguo Li, Milad Radiom, Raffaele Mezzenga , et al. · 2024

Desmoplakin CSM models unravel mechanisms regulating the binding to intermediate filaments and putative therapeutics for cardiocutaneous diseases Open

Cédric Badowski, Paula Benny, Chandra Verma, E. Birgitte Lane · 2024

Desmoplakin CSM models unravel mechanisms regulating the binding to intermediate filaments and putative therapeutics for cardiocutaneous diseases Open

Cédric Badowski, Paula Benny, Chandra Verma, E. Birgitte Lane · 2024

Arrhythmogenic cardiomyopathy (AC) is a severe heart condition that can be fatal during intense exercise or in pregnant women. It is induced by mutation (e.g. R2834H) of the carboxyterminus tail of desmoplakin (DP CT), but the lack of know…

Modulation of<i>Ideonella sakaiensis</i>PETase active site flexibility and activity on morphologically distinct substrates by surface charge engineering Open

Ke Ding, Zarina Levitskaya, Barindra Sana, Rupali Reddy Pasula, Srinivasaraghavan Kannan , et al. · 2024

Enzymatic hydrolysis of polyethylene terephthalate (PET) waste is a compelling strategy for environmentally friendly recycling of a major pollutant. Here, we investigate the effects of surface charge point mutations both proximal and dista…

Expanding the DNA editing toolbox: Novel lambda integrase variants targeting microalgal and human genome sequences Open

Jia Wei Siau, Asim Azhar Siddiqui, Sze Yi Lau, Srinivasaraghavan Kannan, Sabrina Peter , et al. · 2024

Recombinase enzymes are extremely efficient at integrating very large DNA fragments into target genomes. However, intrinsic sequence specificities curtail their use to DNA sequences with sufficient homology to endogenous target motifs. Ext…

Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists Open

Arun Chandramohan, Hubert Josien, Tsz Ying Yuen, Ruchia Duggal, Diana Spiegelberg , et al. · 2024

Design and evaluation of tadpole-like conformational antimicrobial peptides Open

Ziyi Tang, Wuqiao Jiang, Shuangli Li, Xue Huang, Yi Yang , et al. · 2023

Antimicrobial peptides are promising alternatives to conventional antibiotics. Herein, we report a class of “tadpole-like” peptides consisting of an amphipathic α-helical head and an aromatic tail. A structure-activity relationship (SAR) s…

Benchmarking RNA all-atom force fields using hairpin motifs Open

Dimitrios Stamatis, Chandra Verma, Jonathan W. Essex · 2023

Ribonucleic acid (RNA) is a multipotent polymer of great biological and engineering interest. Computer simulations that investigate the structure and dynamics of these molecules are powerful tools for understanding and manipulating their p…

24 Small-molecule regulated safety switch for improved safety of CAR cell therapies in the brain Open

Rebecca Cottman, Vanessa Johnson, Michelle Hung, Yin Yin Chong, Assen Roguev , et al. · 2023

Background The application of CAR T cell therapies have demonstrated success in the clinic in select hematologic malignancies. Their broad utilization has been limited to select centers with specialized care due to risk of Cytokine Release…

A coarse-grained model of glycosaminoglycans for biomolecular simulations Open

Aishwary T. Shivgan, Jan K. Marzinek, Alexander Krah, Paul Matsudaira, Chandra Verma , et al. · 2023

Proteoglycans contain glycosaminoglycans (GAGs), negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, parti…

Expanding the DNA editing toolbox: novel lambda integrase variants targeting microalgal and human genome sequences Open

Siau Jia Wei, Asim Azhar Siddiqui, Lau Sze Yi, inivasaraghavan Kannan, Sabrina Peter , et al. · 2023

Recombinase enzymes are extremely efficient at integrating very large DNA fragments into target genomes. However, intrinsic sequence specificities curtail their use to DNA sequences with sufficient homology to endogenous target motifs. Ext…

Dissecting the geometric and hydrophobic constraints of stapled peptides Open

Jianguo Li, Yaw Sing Tan, Chandra Verma · 2023

Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enh…

JNK mediates cell death by promoting the ubiquitination of the apurinic/apyrimidinic endonuclease APE1 Open

Bahareh Tabanifar, Anbalagan Moorthy, Heng Hang Tsai, Srinivasaraghavan Kannan, Chandra Verma , et al. · 2023

The c-Jun-NH2-terminal kinases (JNKs) regulate cell death, generally through the direct phosphorylation of both pro- and anti-apoptotic substrates. In this report, we demonstrate an alternate mechanism of JNK-mediated cell death involving …

CAMK2D serves as a molecular scaffold for RNF8-MAD2 complex to induce mitotic checkpoint in glioma Open

You Heng Chuah, Emmy Xue Yun Tay, Oleg V. Grinchuk, Jeehyun Yoon, Jia Feng , et al. · 2023

Disrupting the Dok3–Card9 Interaction with Synthetic Peptides Enhances Antifungal Effector Functions of Human Neutrophils Open

Jia Tong Loh, Joey Kay Hui Teo, Srinivasaraghavan Kannan, Chandra Verma, Hong Hwa Lim , et al. · 2023

Invasive fungal disease is an emerging and serious public health threat globally. The expanding population of susceptible individuals, together with the rapid emergence of multidrug-resistant fungi pathogens, call for the development of no…

A high‐throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell‐based assays Open

Stephen H. Kasper, Stephanie Otten, Brian Squadroni, Cionna Orr‐Terry, Yi Kuang , et al. · 2023

Cyclic peptides are poised to target historically difficult to drug intracellular protein–protein interactions, however, their general cell impermeability poses a challenge for characterizing function. Recent advances in microfluidics have…

Nature-inspired synthetic oligourea foldamer channels allow water transport with high salt rejection Open

Chiranjit Dutta, Pannaga Krishnamurthy, Dandan Su, Sung Hyun Yoo, Gavin W. Collie , et al. · 2023

Development of constrained peptide inhibitors targeting an oncogenic E3 ubiquitin ligase Open

Grasilda Zenkevičiūtė, Wenshu Xu, Jessica Iegre, Hikaru Seki, Yaw Sing Tan , et al. · 2023

SCF Skp2/Cks1 is an E3 ubiquitin ligase, whose substrate specificity is determined by the oncogenic F-box protein Skp2 and the adaptor protein Cks1. A principal target of SCF Skp2/Cks1 is the cyclin-dependent kinase inhibitor p27. Elevated…

Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application to Mdm2/X dual antagonists Open

Arun Chandramohan, Hubert Josien, Tsz Ying Yuen, Ruchia Duggal, Diana Spiegelberg , et al. · 2023

Stapled α-helical peptides can bind to and modulate historically intractable targets while addressing the traditional liabilities associated with peptide therapeutics. However, their pipeline advancement has been impeded by the challenges …

Structome: Exploring the structural neighbourhood of proteins Open

Ashar J. Malik, Chandra Verma, Anthony M. Poole, Jane R. Allison · 2023

Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed, that allows users t…

Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D Open

Sebastian Maurer‐Stroh, Ashar J. Malik, Dimitar Kenanov, Cheng‐Shoong Chong, Mert B. Ozturk , et al. · 2023

One of the promises of precision medicine is to understand and act on inter-individual genetic differences in drug responses. SNPdrug3D contains the complete genomic landscape of missense single nucleotide variants (SNV) across the human p…

Covalent Rescue of Mutant p53 Open

David P. Lane, Chandra Verma · 2023

Summary: p53 mutant proteins are widely expressed in human cancer. In this issue, Guiley and Shokat describe the development of compounds that rescue the function of the Y220C mutant p53 protein by forming covalent complexes with the targe…

Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein Open

Clare Jelinska, Srinivasaraghavan Kannan, Yuri Frosi, Siti Radhiah Ramlan, Fernaldo Richtia Winnerdy , et al. · 2023

Interactions between DAXX and numerous protein interaction partners, along with the autoregulation of a DAXX SUMO Interaction Motif (SIM), can be inhibited by stapled and stitched peptides derived from a minimal DAXX binding peptide found …

Structome: a tool for the rapid assembly of datasets for structural phylogenetics Open

Ashar J. Malik, Desiree Langer, Chandra Verma, Anthony M. Poole, Jane R. Allison · 2023

Summary Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed that allows …

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