tag:joss.theoj.org,2005:/papers/tagged/structural%20biologyJournal of Open Source Software2024-02-27T21:24:38ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48132024-02-27T21:24:38Z2024-03-22T14:09:24ZDeepRank2: Mining 3D Protein Structures with Geometric Deep Learningacceptedv2.1.02023-09-22 15:36:51 UTC942024-02-27 21:24:38 UTC920245983GiuliaCrocioniNetherlands eScience Center, Amsterdam, The Netherlands0000-0002-0823-0121DaniL.BodorNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-2109-2349CoosBaakmanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4317-1566FarzanehM.PariziThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4230-7492Daniel-T.RademakerThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-1959-1317GayatriRamakrishnanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0001-8203-2783SvenA.van der BurgNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-1250-6968DarioF.MarzellaThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-0043-3055JoãoM.c.TeixeiraIndependent Researcher0000-0002-9113-0622LiC.XueThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-2613-538X10.21105/joss.05983https://doi.org/10.5281/zenodo.10566809Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05983.pdfPyTorch, structural biology, geometric deep learning, 3D protein structures, protein-protein interfaces, single-residue variants, graph neural networks, convolutional neural networks, DeepRanktag:joss.theoj.org,2005:Paper/39102023-05-10T21:56:30Z2023-05-11T09:10:10ZSPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.acceptedv0.1.102022-09-21 16:08:40 UTC852023-05-10 21:56:30 UTC820234861ZiHaoLiuMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0002-8357-8507OufanZhangPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of AmericaJoãoM.c.TeixeiraDepartment of Biomedical Sciences, University of Padua, Padova, Italy0000-0002-9113-0622JieLiPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America0000-0002-4727-1786TeresaHead-GordonPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America, Department of Bioengineering, University of California, Berkeley, California, United States of America0000-0003-0025-8987JulieD.Forman-KayMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0001-8265-972X10.21105/joss.04861https://doi.org/10.5281/zenodo.7887039Pythonhttps://joss.theoj.org/papers/10.21105/joss.04861.pdfNMR, SAXS, smFRET, Back-calculator, PDB, Structural Biology, Proteins, Biochemistrytag:joss.theoj.org,2005:Paper/32982022-05-04T18:45:45Z2022-05-05T00:00:47ZGEMMI: A library for structural biologyacceptedv0.5.12022-01-19 22:13:15 UTC732022-05-04 18:45:45 UTC720224200MarcinWojdyrGlobal Phasing Ltd., Cambridge, UK0000-0003-3980-409210.21105/joss.04200https://doi.org/10.6084/m9.figshare.19678776C++, Fortranhttps://joss.theoj.org/papers/10.21105/joss.04200.pdfstructural biology, crystallography, CIFtag:joss.theoj.org,2005:Paper/31632022-02-05T08:41:42Z2022-02-06T00:00:29ZCacatoo: building, exploring, and sharing spatially structured models of biological systemsacceptedv1.0.02021-11-09 14:35:39 UTC702022-02-05 08:41:42 UTC720223948Bramvan DijkMax Planck Institute for Evolutionary Biology0000-0002-6330-693410.21105/joss.03948https://doi.org/10.5281/zenodo.5918404JavaScripthttps://joss.theoj.org/papers/10.21105/joss.03948.pdfjavascript, spatial structure, dynamics, individual-based models, microbial ecology and evolutiontag:joss.theoj.org,2005:Paper/15342020-07-09T00:33:17Z2021-02-15T11:30:56Zgraphsim: An R package for simulating gene expression data from graph structures of biological pathwaysaccepted0.1.22020-03-02 07:37:42 UTC512020-07-09 00:33:17 UTC520202161S.ThomasKellyDepartment of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
, RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan0000-0003-3904-6690MichaelA.BlackDepartment of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand0000-0003-1174-605410.21105/joss.02161https://doi.org/10.5281/zenodo.3931288R, Rubyhttps://joss.theoj.org/papers/10.21105/joss.02161.pdfgene-expression, simulation, genomics, pathway, networktag:joss.theoj.org,2005:Paper/15402020-06-03T10:40:49Z2021-02-15T11:30:54Ztaurenmd: A command-line interface for analysis of Molecular Dynamics simulations.acceptedv0.8.92020-03-03 20:18:24 UTC502020-06-03 10:40:49 UTC520202175JoãoM.C.TeixeiraPrevious, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain, Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada0000-0002-9113-062210.21105/joss.02175https://doi.org/10.5281/zenodo.3843326Pythonhttps://joss.theoj.org/papers/10.21105/joss.02175.pdfMolecular Dynamics, Structural Biology, Proteins, DNA, RNA, Biochemistrytag:joss.theoj.org,2005:Paper/2032017-06-07T00:00:00Z2021-02-15T11:34:06ZBioPandas: Working with molecular structures in pandas DataFramesacceptedv2.1.02017-06-01 00:08:43 UTC142017-06-07 00:00:00 UTC22017279SebastianRaschkaMichigan State University, East-Lansing, USA0000-0001-6989-449310.21105/joss.00279https://doi.org/10.5281/zenodo.804030Pythonhttps://joss.theoj.org/papers/10.21105/joss.00279.pdfbioinformatics, computational biology, protein structure analysis, protein-ligand docking, virtual screening