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Comparing intermediate range order for alkyl- vs. ether-substituted cations in ionic liquids
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      KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities

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          Abstract

          Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: a RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.

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          KVFinder-web: A web-based application for cavity detection and characterization of any type of biomolecular structure.

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          VMD: Visual molecular dynamics

          William Humphrey, Andrew Dalke, Klaus Schulten (1996)
          Article 0 comments Cited 5221 times – based on 0 reviews     Review now
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            UCSF ChimeraX : Structure visualization for researchers, educators, and developers

            Eric F. Pettersen, Thomas Goddard, Conrad Huang … (2021)
            UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
            Article 0 comments Cited 2412 times – based on 0 reviews     Review now
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              CASTp 3.0: computed atlas of surface topography of proteins

              Wei Tian, Chang Chen, Xue Lei … (2018)
              Abstract Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.
              Article 0 comments Cited 543 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                João V S Guerra:
                ORCID: https://orcid.org/0000-0002-6800-4425
                Helder V Ribeiro-Filho
                José G C Pereira
                Paulo S Lopes-de-Oliveira:
                ORCID: https://orcid.org/0000-0002-1287-8019
                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 05 July 2023
                Publication date (Electronic): 04 May 2023
                Publication date PMC-release: 04 May 2023
                Volume: 51
                Issue: W1
                Pages: W289-W297
                Affiliations
                Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Campinas, São Paulo, 13083-100, Brazil
                Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas , Campinas, São Paulo, 13083-871, Brazil
                Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Campinas, São Paulo, 13083-100, Brazil
                Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Campinas, São Paulo, 13083-100, Brazil
                Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Campinas, São Paulo, 13083-100, Brazil
                Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas , Campinas, São Paulo, 13083-871, Brazil
                Author notes
                To whom correspondence should be addressed. Tel: +55 19 3512 1267; Email: paulo.oliveira@ 123456lnbio.cnpem.br
                Correspondence may also be addressed to José G.C. Pereira. Tel: +55 19 3512 1255; Email: jose.pereira@ 123456lnbio.cnpem.br

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

                Author information
                https://orcid.org/0000-0002-6800-4425
                https://orcid.org/0000-0002-1287-8019
                Article
                Publisher ID: gkad324
                DOI: 10.1093/nar/gkad324
                PMC ID: 10320092
                PubMed ID: 37140050
                SO-VID: 1dc08e0a-233c-455c-823c-a99587850ae5
                Copyright © © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 17 April 2023
                Date revision received : 03 April 2023
                Date received : 04 March 2023
                Page count
                Pages: 9
                Funding
                Funded by: FAPESP, DOI 10.13039/501100001807;
                Award ID: 2018/00629-0
                Funded by: CNPEM, DOI 10.13039/501100011874;
                Categories
                Subject: AcademicSubjects/SCI00010
                Subject: Web Server Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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