Article
Multidisciplinary Sciences
Germano Heinzelmann, Michael K. Gilson
Summary: BAT.py is a Python tool that automates the calculation of protein-ligand binding free energies using the AMBER simulation package, supporting various binding free energy methods, and can be used inexpensively on common machines. This software can be applied in a high-throughput mode for early-stage drug discovery.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jacob Verburgt, Daisuke Kihara
Summary: Protein structure docking involves predicting the quaternary structure of a protein complex from individual tertiary structures of its subunits, typically done in two main steps: docking the subunits rigidly to form the complex, followed by structure refinement. Benchmarking eight protein structure refinement methods showed that improving the fraction of native contacts between subunits was straightforward, while refining backbone dependent metrics based on Root Mean Square Deviation proved more challenging.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Tin M. Tunjic, Noah Weber, Michael Brunsteiner
Summary: Proteolysis targeting chimeras (PROTACs) are a promising class of drug molecules that have the potential to target previously inaccessible proteins. In this review, we discuss recent advancements in PROTAC design, including linker design, absorption estimation for compounds that violate the rule-of-5, and the generation and ranking of ternary complex structures. Despite being a relatively new field, there are already several models and algorithms available to aid in silico design and accelerate pharmaceutical research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Vishakha Choudhary, Kevin Wu, Zhiyao Zhang, Mark Dulchavsky, Todd Barkman, James C. A. Bardwell, Frederick Stull
Summary: The study reveals that the soil-dwelling bacterium Pseudomonas putida S16 can survive on nicotine as its sole carbon and nitrogen source. The enzymes NicA2 and Pnao, which are members of the flavincontaining amine oxidase family, are shown to be dehydrogenases that use CycN as their electron acceptor.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Mathematics, Applied
Christoph Hunkenschroder, Sebastian Pokutta, Robert Weismantel
Summary: This article discusses the problem of minimizing a convex function over a set using a matrix W and an unknown convex function g. It focuses on separable convex functions and sharp convex functions, and presents a proximity theorem that shows the closeness between integral minimum and continuous minimum for these functions. This theorem plays a key role in developing an algorithm for detecting an integer minimum.
SIAM JOURNAL ON OPTIMIZATION
(2023)
Article
Computer Science, Artificial Intelligence
Vitalii Stebliankin, Azam Shirali, Prabin Baral, Jimeng Shi, Prem Chapagain, Kalai Mathee, Giri Narasimhan
Summary: Computational protein-binding studies play a crucial role in understanding biological processes and developing therapeutics. However, accurately scoring protein binding interfaces remains challenging. This study presents a Transformer-based approach that can distinguish between correct and incorrect protein binding conformations.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Chemistry, Medicinal
Georgios Iakovou, Stephen D. Laycock, Steven Hayward
Summary: Interactive docking allows users to guide and control the docking of biomolecules, beneficial for SBDD and educating students on biomolecular interactions. It introduces DockIT for VR, which models conformational changes within the receptor in real-time.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biology
Elke De Zitter, Nicolas Coquelle, Paula Oeser, Thomas R. M. Barends, Jacques-Philippe Colletier
Summary: Xtrapol8 is a program for automatically extracting structural information of low occupancy states, accelerating and facilitating data processing in kinetic, time-resolved and ligand-based crystallographic studies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Guojun Zhou, Taimin Yang, Zhehao Huang
Summary: This study successfully determined the structure of a low-crystallinity pyrene-containing covalent organic framework using a combination of three-dimensional electron diffraction and simulated annealing.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Physical
Biao Zhang, Wenyi Zhang, Robin Pearce, Yang Zhang, Hong-Bin Shen
Summary: The newly proposed MOFIT protocol utilizes particle swarm optimization to perform rigid-body fitting of cryo-EM density maps, showcasing superior results compared to single-objective function-based methods. The key advantages of MOFIT lie in its multiobjective approach and extensive PSO search simulations, integrating various correlation coefficients for a comprehensive fitting guided by composite objective functions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Neurosciences
Sayan Ghosal, Qiang Chen, Giulio Pergola, Aaron L. Goldman, William Ulrich, Karen F. Berman, Giuseppe Blasi, Leonardo Fazio, Antonio Rampino, Alessandro Bertolino, Daniel R. Weinberger, Venkata S. Mattay, Archana Venkataraman
Summary: The proposed optimization framework integrates imaging and genetics data for biomarker identification and disease classification by projecting data into a shared low dimensional space. The model effectively discriminates between healthy and diseased populations, achieving higher class prediction accuracy and identifying robust biomarkers.
Article
Biochemistry & Molecular Biology
Sameera Sastry Panchangam
Summary: The study focuses on Baby Boom (BBM), a transcription factor that plays a crucial role in embryogenesis, transformation, and development in plants. By conducting in silico analysis, the study aims to understand BBM's sequence and conservation, predict protein interactions and ligands, and determine the binding site residues. Additionally, the study also predicts peptide sequences that interact with BBM, which could be used for further research and design of peptide mimetics.
Article
Chemistry, Analytical
Xinmeng Guo, Jiang Wang
Summary: Acupuncture, an ancient traditional medical treatment, has been hypothesized to have effects mediated through autonomic neural networks. Experimental results show that manual acupuncture stimulation can reduce brain activity dimensionality, enhance oscillatory activity, and lead to similar dynamic attractors in response to acupuncture stimuli across subjects. These findings shed light on the large-scale brain response to manual acupuncture.
Article
Chemistry, Multidisciplinary
Manish Rana, Hungharla Hungyo, Palak Parashar, Shaban Ahmad, Rabiya Mehandi, Vibha Tandon, Khalid Raza, Mohammed A. Assiri, Tarik E. Ali, Zeinhom M. El-Bahy, Rahisuddin
Summary: Researchers designed and synthesized various types of pyrazole analogs for their anticancer and antioxidant activities. The structures of the synthesized analogs were characterized using advanced spectroscopic techniques. One specific analog, 9d, exhibited significant anticancer activity and antioxidant capability. Molecular dynamics simulations were also performed to study the interaction between a specific protein and ligand complex.
Article
Biology
Mohd Afzal, Abdullah Alarifi, Naaser. A. Y. Abduh, Arusha Ayub, Mohd. Muddassir
Summary: Apoptosis is regulated by the BCL-2 family, and inhibition of the pro-apoptotic and anti-apoptotic protein-protein interactions has been studied for developing anticancer drugs. In this study, the hydrophobic nature of 74 organometallic compounds was analyzed, and their effectiveness against the BCL-2 protein was determined using molecular docking. The results identified several important compounds that could bind to the less solvent-accessible site of BCL-2.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Engineering, Electrical & Electronic
O. Borazjani, M. Naser Moghadasi, J. Rashed Mohassel, R. A. Sadeghzadeh
Summary: This study designs a meta-material unit cell with a negative permittivity in the X band and demonstrates its performance through simulation and measurement. The unit shows a negative refractive index within a specific frequency range.
IETE JOURNAL OF RESEARCH
(2022)
Article
Computer Science, Information Systems
Mohammad Alibakhshikenari, Esraa Mousa Ali, Mohammad Soruri, Mariana Dalarsson, Mohammad Naser-Moghadasi, Bal S. Virdee, Caslav Stefanovic, Anna Pietrenko-Dabrowska, Slawomir Koziel, Stanislaw Szczepanski, Ernesto Limiti
Summary: On-chip antennas are small, miniaturized radiating elements that can be integrated inside electronic devices. Recent techniques and technologies have been investigated to improve the performance of on-chip antennas for millimeter-waves and terahertz applications.
Article
Engineering, Civil
Salomon Wollenstein-Betech, Mauro Salazar, Arian Houshmand, Marco Pavone, Ioannis Ch. Paschalidis, Christos G. Cassandras
Summary: This paper explores congestion-aware route-planning policies for intermodal Autonomous Mobility-on-Demand (AMoD) systems, optimizing AMoD routing and rebalancing strategies to improve overall system performance under mixed traffic conditions.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2022)
Article
Biochemical Research Methods
Shahabeddin Sotudian, Ioannis Ch Paschalidis
Summary: This study proposes a machine learning approach to predict drug responses based on patient genomic information. The algorithm compares drug-cell line pairs to rank the effectiveness of different drugs on the same cell line. The proposed approach outperforms state-of-the-art methods, even when a large number of drugs and few cell lines are used.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Operations Research & Management Science
Ruidi Chen, Ioannis Ch Paschalidis
Summary: This paper proposes a distributionally robust optimization formulation with a Wasserstein-based uncertainty set for selecting grouped variables in linear regression and classification problems. The resulting model offers robustness explanations for grouped least absolute shrinkage and selection operator algorithms and highlights the connection between robustness and regularization. The authors prove probabilistic bounds on the out-of-sample loss and the estimation bias, and establish the grouping effect of their estimator. They also propose a method using the spectral clustering algorithm for variable grouping, making their approach applicable without prior knowledge of the grouping structure.
JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS
(2022)
Article
Engineering, Manufacturing
Guanxiong Miao, Mohammadamin Moghadasi, Wenchao Du, Zhijian Pei, Chao Ma
Summary: This experimental investigation explores the impact of roller traverse and rotation speeds on ceramic binder jetting additive manufacturing. Increasing roller traverse speed leads to a decrease in green and sintered densities, with a greater decrease observed at low roller rotation speeds. High roller traverse speeds result in more cavities on the powder bed surface after spreading a new layer and more cracks after jetting the binder. These defects observed during printing persist in the green and sintered parts. Additionally, parts printed at high roller traverse speeds exhibit over 30% higher sintered flexural strength compared to parts printed at low traverse speeds.
JOURNAL OF MANUFACTURING PROCESSES
(2022)
Article
Automation & Control Systems
Shi Pu, Alex Olshevsky, Ioannis Ch Paschalidis
Summary: This article focuses on minimizing the average of cost functions over a network, where agents can communicate and exchange information. The article studies the distributed stochastic gradient descent (DSGD) method when only noisy gradient information is available, and performs a nonasymptotic convergence analysis. The main contribution of the article is to characterize the transient time needed for DSGD to approach the asymptotic convergence rate, and construct a hard optimization problem to prove the sharpness of the obtained result. Numerical experiments demonstrate the tightness of the theoretical results.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Engineering, Manufacturing
Guanxiong Miao, Mohammadamin Moghadasi, Ming Li, Zhijian Pei, Chao Ma
Summary: Shell printing is an advantageous technique that prints a thin shell of the object to enclose loose powder. This study investigated the powder packing in the shell and core for the first time. The density and microstructure of the printed samples showed differences in powder packing between the shell and core, influenced by powder particle size and layer thickness. By selecting the proper layer thickness and powder particle size, shell printing could be a promising method to tailor density and reduce anisotropy.
JOURNAL OF MANUFACTURING AND MATERIALS PROCESSING
(2023)
Article
Medical Informatics
Yang Hu, Jasmine Huerta, Nicholas Cordella, Rebecca G. G. Mishuris, Ioannis Ch. Paschalidis
Summary: This study developed a model based on patient characteristics to recommend antihypertensive medications for personalized treatment. The results showed that this personalized treatment significantly reduced patients' future systolic blood pressure compared to standard care.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2023)
Article
Materials Science, Ceramics
Quinton Porter, Mohammadamin Moghadasi, Zhijian Pei, Chao Ma
Summary: The objective of this study was to evaluate the feasibility of producing metal-free fully ceramic composites using binder jetting of alumina preforms and spontaneous infiltration by copper in air. Different particle sizes of alumina powders were used as feedstock for binder jetting, followed by standard post-processing steps. The sintered specimens were then infiltrated with copper, resulting in improved mechanical properties compared to the porous sintered specimens. The compressive strength of 826.0 MPa and flexural strength of 317.5 MPa achieved in this study exceed those reported in the literature for binder jetting and/or infiltration of alumina-based specimens.
CERAMICS INTERNATIONAL
(2023)
Article
Energy & Fuels
Zonglin Li, Hong Li, Wenhou Li, Jiaopeng Sun, Keyong Li
Summary: The Upper Paleozoic coal-bearing rock series are mainly distributed in the Benxi, Taiyuan, and Shanxi formations. Mudstones and coals are frequently formed in tidal flat deposits. The rocks are thicker on the western, eastern, and northern sides, thinner in the middle, and gradually thinner from north to south. The majority of the coal comprises excellent source rocks, while all limestones are poor source rocks and most mudstones are good-excellent source rocks. The studied source rocks are at the postmature-dry gas stage.
Article
Geochemistry & Geophysics
Haiyan Wu, Ting Liang, Chao Gao, Yanjun Wu, Hongxia Cao, Jun Yu, Fenfei Bai, Jianbo Sun, Keyong Li, Yanqin Guo
Summary: A study was conducted on the Yan'an gas field to examine the natural gas reserves, diagenetic evolution, and different diagenesis environments. The results showed the lithology of the reservoir and the filling materials, as well as the carbon and oxygen isotope values and Sr-87/Sr-86 values. The stratigraphic development indicated a cyclical trend, and the fluid inclusions revealed the sources of fluids in the sedimentation and diagenesis process.
Article
Multidisciplinary Sciences
Shahabeddin Sotudian, Ruidi Chen, Ioannis Ch. Paschalidis
Summary: Despite the satisfactory performance of most existing listwise LTR models, the crucial issue of robustness is often overlooked. In order to fill this gap, a new listwise LTR model called DRMRR is introduced, which incorporates the idea of Distributionally Robust Optimization (DRO) to handle various types of noise and perturbations. The experiments conducted on medical document retrieval and drug response prediction demonstrate that DRMRR outperforms state-of-the-art LTR models and maintains stable performance even with added noise.
Article
Computer Science, Information Systems
Afshin Souzani, Mohammad Ali Pourmina, Paeiz Azmi, Mohammad Naser-Moghadasi
Summary: Intelligence reconfigurable surfaces (IRS) have garnered attention for their ability to create an intelligent and controllable wireless propagation environment, promoting efficient and secure design. Physical layer security (PLS) is a vital technique in wireless networks, ensuring information-theoretic security despite the computational capability of eavesdroppers. The proposed system model combines IRS-assisted NOMA with obstacles hindering direct links, demonstrating enhanced secrecy rate through cooperative jamming signals and increased elements in the IRS, compared to orthogonal multiple access (OMA).
Article
Computer Science, Hardware & Architecture
Yijia Zhang, Daniel Curtis Wilson, Ioannis Ch. Paschalidis, Ayse K. Coskun
Summary: Demand response programs provide monetary incentives to consumers who regulate their power consumption, particularly beneficial for HPC data centers. This study proposes an Adaptive policy with QoS Assurance to enable data centers to participate in regulation service programs while ensuring job QoS. Experimental results show a reduction in electricity costs by 25-56% with QoS assurance.
IEEE TRANSACTIONS ON SUSTAINABLE COMPUTING
(2022)