{"title":"You must be flexible enough to be trained, Mr. Dynamics simulator.","authors":"Ammar Usman Danazumi, Haruna Isiyaku Umar","doi":"10.1007/s11030-023-10689-5","DOIUrl":null,"url":null,"abstract":"<p><p>This article highlights two major problems associated with molecular dynamics studies: poor parameterization of systems and misleading interpretation of data. To address these issues, we advocate for meticulous system parameterization and careful interpretation of statistics within the framework of the study system, with a focus on high-quality and rigorous simulations. Our letter aims to encourage the adoption of the best practices in the field.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Diversity","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1007/s11030-023-10689-5","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/7/12 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, APPLIED","Score":null,"Total":0}
引用次数: 0
Abstract
This article highlights two major problems associated with molecular dynamics studies: poor parameterization of systems and misleading interpretation of data. To address these issues, we advocate for meticulous system parameterization and careful interpretation of statistics within the framework of the study system, with a focus on high-quality and rigorous simulations. Our letter aims to encourage the adoption of the best practices in the field.
期刊介绍：
Molecular Diversity is a new publication forum for the rapid publication of refereed papers dedicated to describing the development, application and theory of molecular diversity and combinatorial chemistry in basic and applied research and drug discovery. The journal publishes both short and full papers, perspectives, news and reviews dealing with all aspects of the generation of molecular diversity, application of diversity for screening against alternative targets of all types (biological, biophysical, technological), analysis of results obtained and their application in various scientific disciplines/approaches including:
combinatorial chemistry and parallel synthesis;
small molecule libraries;
microwave synthesis;
flow synthesis;
fluorous synthesis;
diversity oriented synthesis (DOS);
nanoreactors;
click chemistry;
multiplex technologies;
fragment- and ligand-based design;
structure/function/SAR;
computational chemistry and molecular design;
chemoinformatics;
screening techniques and screening interfaces;
analytical and purification methods;
robotics, automation and miniaturization;
targeted libraries;
display libraries;
peptides and peptoids;
proteins;
oligonucleotides;
carbohydrates;
natural diversity;
new methods of library formulation and deconvolution;
directed evolution, origin of life and recombination;
search techniques, landscapes, random chemistry and more;
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