Muhamed Amin
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View article: Graph Neural Networks Model Based on Atomic Hybridization for Predicting Drug Targets
Graph Neural Networks Model Based on Atomic Hybridization for Predicting Drug Targets Open
Accurate prediction of half-maximal inhibitory concentration (IC 50 ) values is critical for accelerating drug discovery, yet traditional quantitative structure-activity relationship (QSAR) models often have limited ability to capture both…
View article: Machine Learning-Driven Drug Repurposing for KRAS G12C and KRAS G12D Inhibition
Machine Learning-Driven Drug Repurposing for KRAS G12C and KRAS G12D Inhibition Open
KRAS is a predominant oncogenic driver across multiple cancers, long considered “undruggable” due to its high nucleotide affinity and lack of classical binding pockets. Although recent advances have led to covalent inhibitors like Sotorasi…
View article: Boltzmann Classifier: A Thermodynamic-Inspired Approach to Supervised Learning
Boltzmann Classifier: A Thermodynamic-Inspired Approach to Supervised Learning Open
We present the Boltzmann classifier, a novel distance based probabilistic classification algorithm inspired by the Boltzmann distribution. Unlike traditional classifiers that produce hard decisions or uncalibrated probabilities, the Boltzm…
View article: Predicting Iron–Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures
Predicting Iron–Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures Open
Iron-sulfur (Fe-S) clusters are critical cofactors in metalloproteins, essential for cellular processes such as energy production, DNA repair, enzymatic catalysis, and metabolic regulation. While Fe-S cluster functions are intimately linke…
View article: Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features
Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features Open
Here, we use the frequency of the atomic hybridizations (s, sp, sp2, and sp3) of each atom type (H, C, N, O, S, etc.) within a molecule to predict the IC50s of drug-like molecules, focusing on compounds targeting the Thrombin, Estrogen Rec…
View article: An improved simulation methodology for nanoparticle injection through aerodynamic lens systems
An improved simulation methodology for nanoparticle injection through aerodynamic lens systems Open
Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving high-d…
View article: Laser-Induced Alignment of Nanoparticles and Macromolecules for Coherent-Diffractive-Imaging Applications
Laser-Induced Alignment of Nanoparticles and Macromolecules for Coherent-Diffractive-Imaging Applications Open
Laser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with X-ray free-electron lasers [PRL 92, 198102 (2004)]. However, the alignment…
View article: An improved numerical simulation methodology for nanoparticle injection through aerodynamic lens systems
An improved numerical simulation methodology for nanoparticle injection through aerodynamic lens systems Open
Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving high-d…
View article: Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors
Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors Open
The oxygen-evolving complex (OEC) of Photosystem II catalyzes the water-splitting reaction using solar energy. Thus, understanding the reaction mechanism will inspire the design of biomimetic artificial catalysts that convert solar energy …
View article: Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning Open
Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the b…
View article: Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II
Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II Open
In plants and algae, the primary antenna protein bound to photosystem II is light harvesting complex II (LHCII), a pigment-protein complex that binds both chlorophyll (Chl) 𝘢 and Chl 𝘣 molecules. Chl 𝘢 and Chl 𝘣 have similar structures but…
View article: Computing the relative affinity of chlorophylls a and b to light-harvesting complex II
Computing the relative affinity of chlorophylls a and b to light-harvesting complex II Open
In plants and algae, the primary antenna protein bound to photosystem II is light harvesting complex II (LHCII), a pigment-protein complex that binds both chlorophyll (Chl) a and Chl b molecules. Chl a and Chl b have similar structures but…
View article: Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II
Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II Open
Simulation data for MCCE and FEP on Pea (PDB: 2BHW) and Spinach (PDB: 1RWT) LHCII. MCCE step2_out files and the coordinates for the refitted spinach structure. Simulation data for FEP input/output files.
View article: Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II
Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II Open
Simulation data for MCCE and FEP on Pea (PDB: 2BHW) and Spinach (PDB: 1RWT) LHCII. MCCE step2_out files and the coordinates for the refitted spinach structure. Simulation data for FEP input/output files.
View article: Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications
Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications Open
Laser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with x-ray free-electron lasers [PRL 92, 198102 (2004)]. However, the alignment…
View article: Engineering of Molybdenum Sulfide Nanobunches on MWCNTs: Modulation of Active Sites and Electronic Conductivity via Controllable Solvothermal Deposition
Engineering of Molybdenum Sulfide Nanobunches on MWCNTs: Modulation of Active Sites and Electronic Conductivity via Controllable Solvothermal Deposition Open
Amorphous, mixed-valency, molybdenum sulfide (MoSx) with a proposed formula [Mo(IV) 4Mo(V) 2(S2 2-)3(S2-)5](SO4)5, was grown through one-pot, solvothermal synthesis on multi-walled carbon nanotubes (MWCNTs) in a gram-scale setup. Optimizin…
View article: Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment
Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment Open
We show experimental evidence that ionizing radiation is able to cross-link two collagen mimetic peptide triple helices in the gas phase, challenging the previously proposed water-mediated collagen cross-linking mechanism.
View article: Machine Learning Model for Predicting Number of COVID-19 Cases in Countries with Low Number of Tests
Machine Learning Model for Predicting Number of COVID-19 Cases in Countries with Low Number of Tests Open
Background: The COVID-19 pandemic has presented a series of new challenges to governments and healthcare systems. Testing is one important method for monitoring and controlling the spread of COVID-19. Yet with a serious discrepancy in the …
View article: Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning
Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning Open
Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of t…
View article: Toward understanding the S<sub>2</sub>-S<sub>3</sub> transition in the Kok cycle of Photosystem II: Lessons from Sr-substituted structure
Toward understanding the S<sub>2</sub>-S<sub>3</sub> transition in the Kok cycle of Photosystem II: Lessons from Sr-substituted structure Open
Understanding the water oxidation mechanism in Photosystem II (PSII) stimulates the design of biomimetic artificial systems that can convert solar energy into hydrogen fuel efficiently. The Sr2+ substituted PSII is active but slower than w…
View article: Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I
Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I Open
Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the f…
View article: Predicting the Oxidation States of Mn ions in the Oxygen Evolving Complex of Photosystem II Using Supervised and Unsupervised Machine Learning
Predicting the Oxidation States of Mn ions in the Oxygen Evolving Complex of Photosystem II Using Supervised and Unsupervised Machine Learning Open
Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II. However, due to the incoherent transition of the S-st…
View article: The Delta variant mutations in the receptor binding domain of SARS-CoV-2 show enhanced electrostatic interactions with the ACE2
The Delta variant mutations in the receptor binding domain of SARS-CoV-2 show enhanced electrostatic interactions with the ACE2 Open
Mutations in the receptor binding domain (RBD) in SARS-CoV-2 are shown to enhance its replication, transmissibility, and binding to host cells. Recently, a new strain is reported in India that includes a mutation (T478K, and L452R) in the …
View article: Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium
Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium Open
Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetram…