Computational and structural biotechnology journal最新文献

{"title":"A comprehensive overview of recent advances in generative models for antibodies","authors":"Fanxu Meng, Na Zhou, Guangchun Hu, Ruotong Liu, Yuanyuan Zhang, Ming Jing, Qingzhen Hou","doi":"10.1016/j.csbj.2024.06.016","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.016","url":null,"abstract":"Therapeutic antibodies are an important class of biopharmaceuticals. With the rapid development of deep learning methods and the increasing amount of antibody data, antibody generative models have made great progress recently. They aim to solve the antibody space searching problems and are widely incorporated into the antibody development process. Therefore, a comprehensive introduction to the development methods in this field is imperative. Here, we collected 34 representative antibody generative models published recently and all generative models can be divided into three categories: sequence-generating models, structure-generating models, and hybrid models, based on their principles and algorithms. We further studied their performance and contributions to antibody sequence prediction, structure optimization, and affinity enhancement. Our manuscript will provide a comprehensive overview of the status of antibody generative models and also offer guidance for selecting different approaches.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"43 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CORACLE (COVID-19 liteRAture CompiLEr): A platform for efficient tracking and extraction of SARS-CoV-2 and COVID-19 literature, with examples from post-COVID with respiratory involvement","authors":"Kristina Piontkovskaya, Yulian Luo, Pia Lindberg, Jing Gao, Michael Runold, Iryna Kolosenko, Chuan-Xing Li, Åsa M. Wheelock","doi":"10.1016/j.csbj.2024.06.018","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.018","url":null,"abstract":"During the COVID-19 pandemic a need to process large volumes of publications emerged. As the pandemic is winding down, the clinicians encountered a novel syndrome - Post-acute Sequelae of COVID-19 (PASC) - that affects over 10 % of those who contract SARS-CoV-2 and presents a significant challenge in the medical field. The continuous influx of publications underscores a need for efficient tools for navigating the literature. We aimed to develop an application which will allow monitoring and categorizing COVID-19-related literature through building publication networks and medical subject headings (MeSH) maps to identify key publications and networks. We introduce CORACLE (COVID-19 liteRAture CompiLEr), an innovative web application designed to analyse COVID-19-related scientific articles and to identify research trends. CORACLE features three primary interfaces: The \"Search\" interface, which displays research trends and citation links; the \"Citation Map\" interface, allowing users to create tailored citation networks from PubMed Identifiers (PMIDs) to uncover common references among selected articles; and the \"MeSH\" interface, highlighting current MeSH trends and their associations. CORACLE leverages PubMed data to categorize literature on COVID-19 and PASC, aiding in the identification of relevant research publication hubs. Using lung function in PASC patients as a search example, we demonstrate how to identify and visualize the interactions between the relevant publications. CORACLE is an effective tool for the extraction and analysis of literature. Its functionalities, including the MeSH trends and customizable citation mapping, facilitate the discovery of emerging trends in COVID-19 and PASC research.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"51 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A roadmap towards safe and sustainable by design nanotechnology: Implementation for nano-silver-based antimicrobial textile coatings production by ASINA project","authors":"Irini Furxhi ,&nbsp;Massimo Perucca ,&nbsp;Antti Joonas Koivisto ,&nbsp;Rossella Bengalli ,&nbsp;Paride Mantecca ,&nbsp;Alessia Nicosia ,&nbsp;David Burrueco-Subirà ,&nbsp;Socorro Vázquez-Campos ,&nbsp;Elma Lahive ,&nbsp;Magda Blosi ,&nbsp;Jesús Lopez de Ipiña ,&nbsp;Juliana Oliveira ,&nbsp;Marie Carriere ,&nbsp;Claudia Vineis ,&nbsp;Anna Costa","doi":"10.1016/j.csbj.2024.06.013","DOIUrl":"10.1016/j.csbj.2024.06.013","url":null,"abstract":"<div><p>This report demonstrates a case study within the ASINA project, aimed at instantiating a roadmap with quantitative metrics for Safe(r) and (more) Sustainable by Design (SSbD) options. We begin with a description of ASINA’s methodology across the product lifecycle, outlining the quantitative elements within: Physical-Chemical Features (PCFs), Key Decision Factors (KDFs), and Key Performance Indicators (KPIs). Subsequently, we delve in a proposed decision support tool for implementing the SSbD objectives across various dimensions—functionality, cost, environment, and human health safety—within a broader European context. We then provide an overview of the technical processes involved, including design rationales, experimental procedures, and tools/models developed within ASINA in delivering nano-silver-based antimicrobial textile coatings. The result is pragmatic, actionable metrics intended to be estimated and assessed in future SSbD applications and to be adopted in a common SSbD roadmap aligned with the EU’s Green Deal objectives. The methodological approach is transparently and thoroughly described to inform similar projects through the integration of KPIs into SSbD and foster data-driven decision-making. Specific results and project data are beyond this work’s scope, which is to demonstrate the ASINA roadmap and thus foster SSbD-oriented innovation in nanotechnology.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"25 ","pages":"Pages 127-142"},"PeriodicalIF":4.4,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024002095/pdfft?md5=1ad8a920e251f7b99900a7930b1973c1&pid=1-s2.0-S2001037024002095-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141395605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Target repositioning using multi-layer networks and machine learning: The case of prostate cancer","authors":"Milan Picard ,&nbsp;Marie-Pier Scott-Boyer ,&nbsp;Antoine Bodein ,&nbsp;Mickaël Leclercq ,&nbsp;Julien Prunier ,&nbsp;Olivier Périn ,&nbsp;Arnaud Droit","doi":"10.1016/j.csbj.2024.06.012","DOIUrl":"10.1016/j.csbj.2024.06.012","url":null,"abstract":"<div><p>The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"24 ","pages":"Pages 464-475"},"PeriodicalIF":6.0,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024002101/pdfft?md5=e8ab07e9322518bddc67353b175cc15e&pid=1-s2.0-S2001037024002101-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141397314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases","authors":"Christine Rempfer, Sebastian N.W. Hoernstein, Nico van Gessel, Andreas W. Graf, Roxane P. Spiegelhalder, Anne Bertolini, Lennard L. Bohlender, Juliana Parsons, Eva L. Decker, Ralf Reski","doi":"10.1016/j.csbj.2024.06.014","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.014","url":null,"abstract":"Hydroxylation of prolines to 4-trans-hydroxyproline (Hyp) is mediated by prolyl-4 hydroxylases (P4Hs). In plants, Hyps occur in Hydroxyproline-rich glycoproteins (HRGPs), and are frequently -glycosylated. While both modifications are important, for cell wall stability, they are undesired in plant-made pharmaceuticals. Sequence motifs for prolyl-hydroxylation were proposed but did not include data from mosses, such as Physcomitrella. We identified six moss P4Hs by phylogenetic reconstruction. Our analysis of 73 Hyps in 24 secretory proteins from multiple mass spectrometry datasets revealed that prolines near other prolines, alanine, serine, threonine and valine were preferentially hydroxylated. About 95 % of Hyps were predictable with combined established methods. In our data, AOV was the most frequent pattern. A combination of 443 AlphaFold models and MS data with 3000 prolines found Hyps mainly on protein surfaces in disordered regions. Moss-produced human erythropoietin (EPO) exhibited -glycosylation with arabinose chains on two Hyps. This modification was significantly reduced in a knock-out (KO) Physcomitrella mutant. Quantitative proteomics with different mutants revealed specific changes in protein amounts, and a modified prolyl-hydroxylation pattern, suggesting a differential function of the Physcomitrella P4Hs. Quantitative RT-PCR revealed a differential effect of single KOs on the expression of the other five genes, suggesting a partial compensation of the mutation. AlphaFold-Multimer models for Physcomitrella P4H1 and its target EPO peptide superposed with the crystal structure of Chlamydomonas P4H1 suggested significant amino acids in the active centre of the enzyme and revealed differences between P4H1 and the other Physcomitrella P4Hs.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"86 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Instance-level medical image classification for text-based retrieval in a medical data integration center","authors":"Ka Yung Cheng ,&nbsp;Markus Lange-Hegermann ,&nbsp;Jan-Bernd Hövener ,&nbsp;Björn Schreiweis","doi":"10.1016/j.csbj.2024.06.006","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.006","url":null,"abstract":"<div><p>A medical data integration center integrates a large volume of medical images from clinical departments, including X-rays, CT scans, and MRI scans. Ideally, all images should be indexed appropriately with standard clinical terms. However, some images have incorrect or missing annotations, which creates challenges in searching and integrating data centrally. To address this issue, accurate and meaningful descriptors are needed for indexing fields, enabling users to efficiently search for desired images and integrate them with international standards.</p><p>This paper aims to provide concise annotation for missing or incorrectly indexed fields, incorporating essential instance-level information such as radiology modalities (e.g., X-rays), anatomical regions (e.g., chest), and body orientations (e.g., lateral) using a Deep Learning classification model - ResNet50. To demonstrate the capabilities of our algorithm in generating annotations for indexing fields, we conducted three experiments using two open-source datasets, the ROCO dataset, and the IRMA dataset, along with a custom dataset featuring SNOMED CT labels. While the outcomes of these experiments are satisfactory (Precision of &gt;75%) for less critical tasks and serve as a valuable testing ground for image retrieval, they also underscore the need for further exploration of potential challenges. This essay elaborates on the identified issues and presents well-founded recommendations for refining and advancing our proposed approach.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"24 ","pages":"Pages 434-450"},"PeriodicalIF":6.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024002034/pdfft?md5=bd1fa074436c095e9ca887e9e8641a81&pid=1-s2.0-S2001037024002034-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141323309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical simulation study of nanoparticle diffusion in gray matter","authors":"Peiqian Chen ,&nbsp;Bing Dong ,&nbsp;Weiwu Yao","doi":"10.1016/j.csbj.2024.06.002","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.002","url":null,"abstract":"<div><h3>Purpose</h3><p>Nanomedicine-based approaches have shown great potential in the treatment of central nervous system diseases. However, the fate of nanoparticles (NPs) within the brain parenchyma has not received much attention. The complexity of the microstructure of the brain and the invisibility of NPs make it difficult to study NP transport within the grey matter. Moreover, regulation of NP delivery is not fully understood.</p></div><div><h3>Methods</h3><p>2D interstitial system (ISS) models reflecting actual extracellular space (ECS) were constructed. A particle tracing model was used to simulate the diffusion of the NPs. The effect of NP size on NP diffusion was studied using numerical simulations. The diffusion of charged NPs was explored by comparing experimental and numerical simulation data, and the effect of cell membrane potential on the diffusion of charged NPs was further studied.</p></div><div><h3>Results</h3><p>The model was verified using previously published experimental data. Small NPs could diffuse efficiently into the ISS. The diffusion of charged NPs was hindered in the ISS. Changes in cell membrane potential had little effect on NP diffusion.</p></div><div><h3>Conclusion</h3><p>This study constructed 2D brain ISS models that reflected the actual ECS and simulated the diffusion of NPs within it. The study found that uncharged small NPs could effectively diffuse within the ISS and that the cell membrane potential had a limited effect on the diffusion of charged NPs. The model and findings of this study can aid the design of nanomedicines and nanocarriers for the diagnosis and treatment of brain diseases.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"25 ","pages":"Pages 95-104"},"PeriodicalIF":6.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001995/pdfft?md5=e0a2801bf26e2243ba4d4d7cda644491&pid=1-s2.0-S2001037024001995-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141313388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the impact of the SMARTCLAP project on habilitation","authors":"Matthew Bonello,&nbsp;Nathalie Buhagiar,&nbsp;Philip Farrugia,&nbsp;Joseph Mercieca","doi":"10.1016/j.csbj.2024.06.001","DOIUrl":"10.1016/j.csbj.2024.06.001","url":null,"abstract":"<div><p>This report summarises the SMARTCLAP research project, which employs a user-centred design approach to develop a revolutionary smart product service system. The system offers personalised motivation to encourage children with cerebral palsy to actively participate more during their occupational therapy sessions, while providing paediatric occupational therapists with an optimal tool to monitor children’s progress from one session to another. The product service system developed includes of a smart wearable device called DigiClap used to interact with a serious game in an Augmented Reality environment. The report highlights the research methodology used to advance the technology readiness level from 4 to 6, acknowledging the contribution of the consortium team and funding source. As part of the technology’s maturity process, DigiClap and the respective serious game were evaluated with target users, to identify the system’s impact in supporting the children’s overall participation and hand function, and to gather feedback from occupational therapists and caregivers on this novel technology. The outcomes of this study are discussed, highlighting limitations and lessons learned. The report also outlines future work and further funding for the sustainability of the project and to reach other individuals who have upper limb limitations. Ultimately, the potential of DigiClap and the overall achievements of this project are discussed.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"24 ","pages":"Pages 451-463"},"PeriodicalIF":6.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001983/pdfft?md5=11b063bec7e9ada9f093ebc6cd45f4a4&pid=1-s2.0-S2001037024001983-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141279507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030)","authors":"Flemming R. Cassee ,&nbsp;Eric A.J. Bleeker ,&nbsp;Cyrille Durand ,&nbsp;Thomas Exner ,&nbsp;Andreas Falk ,&nbsp;Steffi Friedrichs ,&nbsp;Elisabeth Heunisch ,&nbsp;Martin Himly ,&nbsp;Sabine Hofer ,&nbsp;Norbert Hofstätter ,&nbsp;Danail Hristozov ,&nbsp;Penny Nymark ,&nbsp;Anna Pohl ,&nbsp;Lya G. Soeteman-Hernández ,&nbsp;Blanca Suarez-Merino ,&nbsp;Eugenia Valsami-Jones ,&nbsp;Monique Groenewold","doi":"10.1016/j.csbj.2024.05.018","DOIUrl":"10.1016/j.csbj.2024.05.018","url":null,"abstract":"<div><p>The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"25 ","pages":"Pages 105-126"},"PeriodicalIF":6.0,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001612/pdfft?md5=3bfe4c5dc0d32dcf2dae7bb35bbf05cb&pid=1-s2.0-S2001037024001612-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141275626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform","authors":"Alfonso Cabezón ,&nbsp;Fabián Suárez-Lestón ,&nbsp;Juan R. Granja ,&nbsp;Ángel Piñeiro ,&nbsp;Rebeca Garcia-Fandino","doi":"10.1016/j.csbj.2024.05.044","DOIUrl":"10.1016/j.csbj.2024.05.044","url":null,"abstract":"<div><p>The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at <span>http://cyclopep.com/</span><svg><path></path></svg></p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"25 ","pages":"Pages 91-94"},"PeriodicalIF":6.0,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001892/pdfft?md5=e402d6fd21dd2d604ec1bb1695841fa1&pid=1-s2.0-S2001037024001892-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141280471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}