Di Jiang, Sarah H. Ross, Bianca Lopez, Sumin Jin, Marc S. Lavine, Ekeoma Uzogara, Jake S. Yeston
{"title":"In Other Journals","authors":"Di Jiang, Sarah H. Ross, Bianca Lopez, Sumin Jin, Marc S. Lavine, Ekeoma Uzogara, Jake S. Yeston","doi":"10.1126/science.adu2105","DOIUrl":"10.1126/science.adu2105","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.science.org/doi/reader/10.1126/science.adu2105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Britain’s postwar sugar craze confirms harms of sweet diets","authors":"Catherine Offord","doi":"10.1126/science.adu2385","DOIUrl":"10.1126/science.adu2385","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.science.org/doi/reader/10.1126/science.adu2385","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raul Ramos, Valerii Plotnikov, Maksim Y. Cheprasov, Maksim V. Plikus
{"title":"Secure ancient animal remains from permafrost","authors":"Raul Ramos, Valerii Plotnikov, Maksim Y. Cheprasov, Maksim V. Plikus","doi":"10.1126/science.adr6701","DOIUrl":"10.1126/science.adr6701","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Charalampos G. Livas, Pantelis N. Trikalitis, George E. Froudakis
{"title":"MOFSynth: A Computational Tool toward Synthetic Likelihood Predictions of MOFs","authors":"Charalampos G. Livas, Pantelis N. Trikalitis, George E. Froudakis","doi":"10.1021/acs.jcim.4c01298","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c01298","url":null,"abstract":"In the past decade, high-throughput computational studies of materials have increased significantly mainly due to advances in computer capabilities and have attracted a great deal of interest. In the field of metal–organic frameworks (MOFs), over a million hypothetical MOFs have been designed in silico, yet only a small fraction of these have been synthesized. For validating the computational-hypothetical results and accelerating the progress in the field, there is a pressing need for distinguishing MOFs that are more likely to be synthesized for real-life applications. This study presents a comprehensive investigation into the synthesizability likelihood of MOFs, utilizing a novel computational approach based on the disparities in energy and geometry between the linker conformation within the MOF structure and its isolated, free-gas state since both of these have been proven to be critical factors influencing MOF synthesis. Our user-friendly tool streamlines synthesizability evaluation, requiring minimal expertise in computational chemistry. By deconstructing over 40,000 MOFs from databases, including QMOF, CoRE MOF, and ToBaCCo, we analyze key parameters defining the linker strain within the MOF unit cell. Our results indicate that QMOF and CoRE MOF contain more promising candidates for synthesis, while ToBaCCo exhibits a relatively poor synthesizability likelihood due to unoptimized materials. Through extensive analysis, we identify optimal linker candidates for highly synthesizable MOFs. Consistent trends in energy distribution across databases that are confirmed by high Pearson and Spearman coefficients suggest the potential for omitting optimization calculations, significantly reducing computational costs. This study underscores the importance of linker deformation and energy disparities and enhances our understanding of synthetic accessibility in MOF research, offering valuable insights for future advancements in the field.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"43 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Generating Multistate Conformations of P-type ATPases with a Conditional Diffusion Model.","authors":"Jingtian Xu, Yong Wang","doi":"10.1021/acs.jcim.4c01519","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c01519","url":null,"abstract":"<p><p>Understanding and predicting the diverse conformational states of membrane proteins is essential for elucidating their biological functions. Despite advancements in computational methods, accurately capturing these complex structural changes remains a significant challenge. Here, we introduce a computational approach to generate diverse and biologically relevant conformations of membrane proteins using a conditional diffusion model. Our approach integrates forward and backward diffusion processes, incorporating state classifiers and additional conditioners to control the generation gradient of conformational states. We specifically targeted the P-type ATPases, a critical family of membrane transporters, and constructed a comprehensive data set through a combination of experimental structures and molecular dynamics simulations. Our model, incorporating a graph neural network with specialized membrane constraints, demonstrates exceptional accuracy in generating a wide range of P-type ATPase conformations associated with different functional states. This approach represents a meaningful step forward in the computational generation of membrane protein conformations using AI and holds promise for studying the dynamics of other membrane proteins.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Keeping outbreaks at bay","authors":"Kanya Long","doi":"10.1126/science.ads1863","DOIUrl":"10.1126/science.ads1863","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ke Chen, Yu Sun, Tong Ni, Li Zhu, Hongsheng Gui, Fanglin Guan
{"title":"Age effects challenge psychiatric research","authors":"Ke Chen, Yu Sun, Tong Ni, Li Zhu, Hongsheng Gui, Fanglin Guan","doi":"10.1126/science.adr6955","DOIUrl":"10.1126/science.adr6955","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacteria divide to conquer antibiotics","authors":"Ewan Harrison","doi":"10.1126/science.adt0042","DOIUrl":"10.1126/science.adt0042","url":null,"abstract":"<div >Antibiotics are a cornerstone of modern medicine, and consequently, antibiotic resistance is a serious public health threat to treating bacterial infections. Shortly after penicillin came into clinical use to treat <i>Staphylococcus aureus</i>—a pathogen that can cause mild to fatal infections—strains resistant to the drug emerged. In 1959, the antibiotic methicillin was introduced to treat penicillin-resistant strains of <i>S. aureus</i>. Methicillin is a member of the β-lactam family of antibiotics that are broadly effective against many types of bacteria. However, by 1960, infections with methicillin-resistant <i>S. aureus</i> (MRSA) had been reported (<i>1</i>). Given the importance of β-lactams for treating <i>S. aureus</i> infections, researchers have sought to understand the mechanism and evolutionary origins of this resistance. On page 573 of this issue, Adedeji-Olulana <i>et al</i>. (<i>2</i>) report that high-level resistance to methicillin requires <i>S. aureus</i> to use a distinct form of cell division to ensure its survival.</div>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bright excitons in black phosphorus","authors":"Milorad V. Milošević, Lucian Covaci","doi":"10.1126/science.adt0451","DOIUrl":"10.1126/science.adt0451","url":null,"abstract":"<div >Excitons—neutral bound states of electron and hole pairs—are essential to the optoelectronic behavior of semiconductor materials. These “quasiparticles” are generated when incident light is absorbed by a semiconductor, and they can recombine to emit light. Understanding and controlling excitonic behavior is therefore crucial to advancing nanophotonic and quantum optoelectronic technologies. However, presently available materials for such devices often do not exhibit a strong-enough interaction with light and lack tunability. On page 526 of this issue, Huang <i>et al</i>. (<i>1</i>) report the unexpected emergence of strong dipolar excitons in twisted multilayers of black phosphorus. This material exhibits tunable excitonic properties, which could unlock new quantum phenomena and shape future technologies.</div>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"NextGen Voices: Quarter-Century Haiku","authors":"","doi":"10.1126/science.adu2108","DOIUrl":"10.1126/science.adu2108","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"386 6721","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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