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Author Details

Mohammad R K Mofrad
University of California Berkeley
2001
171
41
PMIDPaper TitleJournal TitlePublished Year
37306472On the interactions of peptides with gold nanoparticles: effects of sequence and size.J Biomol Struct Dyn2024
36735895On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study.J Chem Inf Model2023
37924205Force transmission and SUN-KASH higher-order assembly in the LINC complex models.Biophys J2023
37025664A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication.RSC Adv2023
37312993Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication.RSC Adv2023
36786404GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.Bioinformatics2023
36875738Gut-on-a-chip models for dissecting the gut microbiology and physiology.APL Bioeng2023
36935640Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose.ACS Appl Bio Mater2023
36682462On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation.Virus Res2023
36935143Smartphone-assisted lab-in-a-tube device using gold nanocluster-based aptasensor for detection of MUC1-overexpressed tumor cells.Anal Chim Acta2023
34460382TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks.IEEE/ACM Trans Comput Biol Bioinform2022
35806371Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation.Int J Mol Sci2022
36367820Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles.J Phys Chem B2022
36330201Design of a flexing organ-chip to model <i>in situ</i> loading of the intervertebral disc.Biomicrofluidics2022
36299869Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases.Front Cardiovasc Med2022
35218721A short HLA-DRA isoform binds the HLA-DR2 heterodimer on the outer domain of the peptide-binding site.Arch Biochem Biophys2022
35308827On the nuclear pore complex and its emerging role in cellular mechanotransduction.APL Bioeng2022
34931518Acid-Sensitive Surfactants Enhance the Delivery of Nucleic Acids.Mol Pharm2022
35231567Methylation at a conserved lysine residue modulates tau assembly and cellular functions.Mol Cell Neurosci2022
32986852A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain.Immunology2021
33756413Hydrodynamic interactions significantly alter the dynamics of actin networks and result in a length scale dependent loss modulus.J Biomech2021
33667883Intranuclear strain in living cells subjected to substrate stretching: A combined experimental and computational study.J Biomech2021
33630862PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.PLoS One2021
34473567Nucleoporins' exclusive amino acid sequence features regulate their transient interaction with and selectivity of cargo complexes in the nuclear pore.Mol Biol Cell2021
34639238Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex.Int J Mol Sci2021
34327241Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-<i>α</i> Protein.Biomed Res Int2021
34180989EpitopeVec: linear epitope prediction using deep protein sequence embeddings.Bioinformatics2021
34152389Molecular models of LINC complex assembly at the nuclear envelope.J Cell Sci2021
34237287FG nucleoporins feature unique patterns that distinguish them from other IDPs.Biophys J2021
34339633Free energy calculations shed light on the nuclear pore complex's selective barrier nature.Biophys J2021
32191864Kindlin Assists Talin to Promote Integrin Activation.Biophys J2020
32048461Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics.EMBO Mol Med2020
33110113Machine learning for endoleak detection after endovascular aortic repair.Sci Rep2020
33126127Quantification of human sperm concentration using machine learning-based spectrophotometry.Comput Biol Med2020
32709660Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease.J Immunol2020
32181337Nanoscale integrin cluster dynamics controls cellular mechanosensing via FAKY397 phosphorylation.Sci Adv2020
30500871DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.Bioinformatics2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
30099528MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.Bioinformatics2019
31353240Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1.Structure2019
31451222Talin is required to increase stiffness of focal molecular complex in its early formation process.Biochem Biophys Res Commun2019
30837494Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX).Sci Rep2019
31010726Sex-specific Tau methylation patterns and synaptic transcriptional alterations are associated with neural vulnerability during chronic neuroinflammation.J Autoimmun2019
31002996The nucleus feels the force, LINCed in or not!Curr Opin Cell Biol2019
30912802Bridging Finite Element and Machine Learning Modeling: Stress Prediction of Arterial Walls in Atherosclerosis.J Biomech Eng2019
30819565Kindlin Is Mechanosensitive: Force-Induced Conformational Switch Mediates Cross-Talk among Integrins.Biophys J2019
30995155Role of KASH domain lengths in the regulation of LINC complexes.Mol Biol Cell2019
29272321The "Stressful" Life of Cell Adhesion Molecules: On the Mechanosensitivity of Integrin Adhesome.J Biomech Eng2018
29995584A molecular model for LINC complex regulation: activation of SUN2 for KASH binding.Mol Biol Cell2018
29882969Agent-Based Modeling in Molecular Systems Biology.Bioessays2018
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Collaborators

Ehsaneddin Asgari
University of California berkeley
Co-authored papers 11
Alice C McHardy
Computational Biology of Infection Research, Helmholtz Centre for Infection Research
Co-authored papers 9
Jorge R Oksenberg
Co-authored papers 4
Jill A Hollenbach
Weill Institute for Neurosciences, University of California San Francisco
Co-authored papers 3
Gaurav Kumar
Gladstone Institutes
Co-authored papers 2
Nicusor Iftimia
Physical Science Inc.
Co-authored papers 2
Melanie Ott
Gladstone Institute of Virology
Co-authored papers 2
Ursula Schulze-Gahmen
Gladstone Institute of Virology, Gladstone Institutes San Francisco CA USA .
Co-authored papers 2
Daniel K Nomura
University of California berkeley
Co-authored papers 2
Naihui Zhou
The First Affiliated Hospital of Soochow University
Co-authored papers 1
Larry Davis
Co-authored papers 1
Radoslav Davidovic
Institute of Nuclear Sciences Vinca, University of Belgrade
Co-authored papers 1
Sa??o D??eroski
Jozef Stefan Institute
Co-authored papers 1
Domenico Cozzetto
Imperial College London
Co-authored papers 1
Marco Mesiti
Universita degli Studi di Milano
Co-authored papers 1
Neven Sumonja
Institute of Nuclear Sciences VINCA, University of Belgrade
Co-authored papers 1
Magdalena Kotlicka-Antczak
Medical University of Lodz
Co-authored papers 1
Alan J Medlar
Co-authored papers 1
Rui Fa
University College London
Co-authored papers 1
Rahul K Suryawanshi
Gladstone Institutes
Co-authored papers 1
Andreas Bremges
Co-authored papers 1
Sabeur Aridhi
Universite de Lorraine, CNRS
Co-authored papers 1
Qizhong Mao
Temple University
Co-authored papers 1
Michael Detmar
Institute of Pharmaceutical Sciences, ETH Zurich
Co-authored papers 1
Fabio Fabris
University of Kent
Co-authored papers 1
Wei-Cheng Tseng
Taipei Veterans General Hospital
Co-authored papers 1
Christophe Dessimoz
University of Lausanne
Co-authored papers 1
Gage S Black
Brigham Young University
Co-authored papers 1
Suyang Dai
Fudan University
Co-authored papers 1
Maxat Kulmanov
King Abdullah University of Science and Technology.
Co-authored papers 1
Release 1.2