1,720,957 research outputs found
for automated quantum chemistry calculations
No full textThe accuracy of quantum mechanics (QM) simulations depends heavily on the quality of initial input files. Despite the popularity of QM simulation packages, achieving precise results still heavily relies on the user's proficiency in preparing the QM simulation systems. In this work, we present an easy-to-use tool called GUIDE, a YASARA plugin to assist researchers in quantum chemistry workflow automation using ORCA and MOPAC simulation packages. GUIDE lets users compute complex QM calculation workflows via an automated graphical window system. It allows for a more integrated and streamlined research process, as researchers can easily access all the necessary tools within one software without switching between multiple programs. This tool can save time and increase efficiency in computational chemistry methods. GUIDE is written in Python and is freely available for download at . The plugin is released under a GPL-3.0 license and is supported on Windows and Linux
Advancements and novel approaches in modified AutoDock Vina algorithms for enhanced molecular docking
No full textMolecular docking plays a crucial role in modern drug discovery by facilitating the prediction of interactions between small molecules and biomolecular targets. AutoDock Vina (Vina) has earned its reputation as a leading software thanks to its effective energy-based scoring system and user-friendly interface. However, the growing demands of computational biology have prompted investigations into improvements for Vina, leading to a range of algorithmic enhancements. This systematic review explores the recent developments achieved by Vina for molecular docking. These modifications include hybrid parallelization methods utilizing high-performance computing and innovative scoring functions integrated with machine learning. The review examines the difficulties and possibilities associated with these adapted algorithms, shedding light on their diverse origins and potential collaboration across computational chemistry, machine learning, structural biology, and emerging technologies
YAMACS: A Python Based Tool Kit for GROMACS
No full textMolecular dynamics (MD) is a powerful tool used to study the evolution of molecular
systems and predict their properties from the inherent interactions. GROMACS is a famous tool for
MD and developed as open-source software. GROMACS is run from the command line with userprovided configuration files. However, the absence of a graphical user interface (GUI) of GROMACS
and proper protocol to develop the input files (Ex: itp files, topology files, etc.) prevent the researcher
from visualizing the MD trajectory in a real-time manner as well as addressing the structural problem.
This issue was addressed by developing a graphical user interface of GROMACS as plugins for
the YASARA molecular graphics suite, called YAMACS. YAMACS is an open-source project and is
available on GitHub. The tool can perform MD simulations for protein, protein–ligand complexes,
membrane–protein complexes, membrane–protein complexes, and small molecule systems. Easily
YAMACS automatizes several steps of input file preparation and allows visualizing the MD trajectory
in real-time. At this conference, I will present the application of YAMACS to simulate the complex
sphingomyelin/POPC embedded in a membrane of POPC. I will also introduce a collaborative
platform to create an open community of users and developers, extend the functionalities of YAMACS,
and improve the quality of computational drug design studies
YAMACS: a graphical interface for GROMACS
No full textA graphical user interface for the GROMACS program has been developed as plugins for YASARA molecular graphics suite. The most significant GROMACS methods can be run entirely via a windowed menu system, and the results are shown on screen in real time
Theoretical investigation of hydroxylated analogues of valinomycin as potassium transporter
Full text link: Valinomycin is a potent ionophore known for its ability to transport potassium ions across biological membranes. The study focuses on the hydroxylated analogues of valinomycin (HyVLMs) and compares their energy profiles and capabilities for transporting potassium ions across phospholipid membranes. Using metadynamics, we investigated the energy profiles of wildtype valinomycin (VLM_1) and its three hydroxylated analogues (VLM_2, VLM_3, and VLM_4). We observed that all analogues exhibited energy maxima in the centre of the membrane and preferred positions below the phospholipid heads. Furthermore, the entry barriers for membrane penetration were similar among the analogues, suggesting that the hydroxyl group did not significantly affect their passage through the membrane. Transition state calculations provided insights into the ability of valinomycin analogues to capture potassium ions, with VLM_4 showing the lowest activation energy and VLM_2 displaying the highest. Our findings contribute to understanding the mechanisms of potassium transport by valinomycin analogues and highlight their potential as ionophores. The presence of the hydroxyl group is of particular importance because it paves the way for subsequent chemical modifications and the synthesis of new antiviral agents with reduced intrinsic toxicity
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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