AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.
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Double layers optimal scheduling of distribution networks and photovoltaic charging and storage station cluster based on leader follower game theory.
Sci Rep
January 2025
Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal Husbandry University, Linzhi, 860000, China.
The paper addresses the economic operation optimization problem of photovoltaic charging-swapping-storage integrated stations (PCSSIS) in high-penetration distribution networks. It proposes a dual-layer optimization scheduling model for PCSSIS clusters and distribution network systems. Firstly, a master-slave game model is constructed.
View Article and Find Full Text PDFAccuracy of robot-assisted implant surgery versus freehand placement: a retrospective clinical study.
Int J Implant Dent
January 2025
Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
Purpose: This study evaluated the accuracy of implant placement using a robotic system (Remebot) compared to freehand surgery and explored factors influencing accuracy.
Methods: This retrospective study included 95 implants placed in 65 patients, divided into robot-assisted (50 implants) and freehand (45 implants) groups. Platform, apical, and angular deviations were measured by superimposing preoperative plans and the postoperative CBCT images.
Background: Subtle changes in naturalistic language have been associated with cognitive abilities in older adults. This study explored script generation as a method for detection of mild cognitive impairment (MCI). Differences in human-coded speech analysis of scripts were examined between MCI vs.
View Article and Find Full Text PDFQuick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry.
J Chem Inf Model
January 2025
Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States.
Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations.
View Article and Find Full Text PDFGPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites.
Brief Bioinform
November 2024
Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan, Hubei 430074, China.
Protein phosphorylation is dynamically and reversibly regulated by protein kinases and protein phosphatases, and plays an essential role in orchestrating a wide range of biological processes. Although a number of tools have been developed for predicting kinase-specific phosphorylation sites (p-sites), computational prediction of phosphatase-specific dephosphorylation sites remains to be a great challenge. In this study, we manually curated 4393 experimentally identified site-specific phosphatase-substrate relationships for 3463 dephosphorylation sites occurring on phosphoserine, phosphothreonine, and/or phosphotyrosine residues, from the literature and public databases.
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