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@Article{ Agirre2023TheCCP4Suite,
author = {Agirre, J and Atanasova, M and Bagdonas, H and Ballard, CB
and Basl{\'e}, A and Beilsten-Edmands, J and Borges, RJ and
Brown, DG and Burgos-M{\'a}rmol, JJ and Berrisford, JM and
others},
title = {The CCP4 suite: integrative software for macromolecular
crystallography},
doi = {10.1107/S2059798323003595},
number = {6},
pages = {449--461},
volume = {79},
abstract = {The Collaborative Computational Project No. 4 (CCP4) is a
UK-led international collective with a mission to develop,
test, distribute and promote software for macromolecular
crystallography. The CCP4 suite is a multiplatform
collection of programs brought together by familiar
execution routines, a set of common libraries and graphical
interfaces. The CCP4 suite has experienced several
considerable changes since its last reference article,
involving new infrastructure, original programs and
graphical interfaces. This article, which is intended as a
general literature citation for the use of the CCP4
software suite in structure determination, will guide the
reader through such transformations, offering a general
overview of the new features and outlining future
developments. As such, it aims to highlight the individual
programs that comprise the suite and to provide the latest
references to them for perusal by crystallographers around
the world.},
file = {:Agirre2023TheCCP4SuiteIntegrativeSoftwareForMacromolecularCrystallography.pdf:PDF},
journal = {Acta Crystallographica Section D: Structural Biology},
keywords = {Collaborative Computational Project No. 4; CCP4;
crystallography software; macromolecular crystallography},
publisher = {International Union of Crystallography},
year = {2023}
}
@InProceedings{ Ansel2024Pytorch,
author = {Jason Ansel and Edward Yang and Horace He and Natalia
Gimelshein and Animesh Jain and Michael Voznesensky and Bin
Bao and Peter Bell and David Berard and Evgeni Burovski and
Geeta Chauhan and Anjali Chourdia and Will Constable and
Alban Desmaison and Zachary DeVito and Elias Ellison and
Will Feng and Jiong Gong and Michael Gschwind and Brian
Hirsh and Sherlock Huang and Kshiteej Kalambarkar and
Laurent Kirsch and Michael Lazos and Mario Lezcano and
Yanbo Liang and Jason Liang and Yinghai Lu and C. K. Luk
and Bert Maher and Yunjie Pan and Christian Puhrsch and
Matthias Reso and Mark Saroufim and Marcos Yukio Siraichi
and Helen Suk and Shunting Zhang and Michael Suo and Phil
Tillet and Xu Zhao and Eikan Wang and Keren Zhou and
Richard Zou and Xiaodong Wang and Ajit Mathews and William
Wen and Gregory Chanan and Peng Wu and Soumith Chintala},
title = {PyTorch 2: Faster Machine Learning Through Dynamic Python
Bytecode Transformation and Graph Compilation},
booktitle = {Proceedings of the 29th ACM International Conference on
Architectural Support for Programming Languages and
Operating Systems, Volume 2},
year = 2024,
pages = {nil},
doi = {10.1145/3620665.3640366},
url = {http://dx.doi.org/10.1145/3620665.3640366},
date_added = {Mon Jul 22 13:58:03 2024},
month = 4
}
@Article{ Battye2011IMOSFLMANewGraphicalInterfaceForDiffractionImageProcessingWithMOSFLM,
author = {Battye, T. G. and Kontogiannis, L. and Johnson, O. and
Powell, H. R. and Leslie, A. G.},
title = {iMOSFLM: a new graphical interface for diffraction-image
processing with MOSFLM},
note = {[PubMed
Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069742}{PMC3069742}]
[DOI:\href{http://dx.doi.org/10.1107/S0907444910048675}{10.1107/S0907444910048675}]
[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21460445}{21460445}]},
number = {Pt 4},
pages = {271-281},
volume = {67},
abstract = {iMOSFLM is a graphical user interface to the diffraction
data-integration program MOSFLM. It is designed to simplify
data processing by dividing the process into a series of
steps, which are normally carried out sequentially. Each
step has its own display pane, allowing control over
parameters that influence that step and providing graphical
feedback to the user. Suitable values for integration
parameters are set automatically, but additional menus
provide a detailed level of control for experienced users.
The image display and the interfaces to the different tasks
(indexing, strategy calculation, cell refinement,
integration and history) are described. The most important
parameters for each step and the best way of assessing
success or failure are discussed.},
endnotereftype= {Journal Article},
file = {:Battye2011IMOSFLMANewGraphicalInterfaceForDiffractionImageProcessingWithMOSFLM.pdf:PDF},
journal = {Acta Crystallogr. D Biol. Crystallogr.},
month = {Apr},
owner = {blaine-mooers},
shorttitle = {iMOSFLM: a new graphical interface for diffraction-image
processing with MOSFLM},
year = {2011}
}
@Article{ Brunger1992FreeRValueANovelStatisticalQuantityForAssessingTheAccuracyOfCrystalStructures,
author = {Brunger, A. T.},
title = {{{F}ree {R} value: a novel statistical quantity for
assessing the accuracy of crystal structures}},
journal = {Nature},
year = {1992},
volume = {355},
number = {6359},
pages = {472--475},
month = {Jan}
}
@Article{ Brunger1992FreeRValueANovelStatisticalQuantityForAssessingTheAccuracyOfCrystalStructures,
author = {Axel T. Br{\"u}nger},
title = {Free R Value: a Novel Statistical Quantity for Assessing
the Accuracy of Crystal Structures},
journal = {Nature},
volume = 355,
number = 6359,
pages = {472-475},
year = 1992,
doi = {10.1038/355472a0},
url = {http://dx.doi.org/10.1038/355472a0},
date_added = {Sun Jul 21 06:19:59 2024},
file = {:Brunger1992FreeRValueANovelStatisticalQuantityForAssessingTheAccuracyOfCrystalStructures.pdf:PDF}
}
@Article{ Burla2024UpdatingDirectMethodsII,
author = {Maria Cristina Burla and Carmelo Giacovazzo and Giampiero
Polidori},
title = {Updating Direct Methods Ii. Reduction of the Structural
Complexity When Triplet Invariants Are Estimated Via the
Patterson Map},
journal = {Journal of Applied Crystallography},
volume = 57,
number = 4,
pages = {nil},
year = 2024,
doi = {10.1107/s1600576724004345},
url = {http://dx.doi.org/10.1107/S1600576724004345},
date_added = {Fri Jul 19 12:32:37 2024},
file = {:Burla2024UpdatingDirectMethodsII.pdf:PDF}
}
@Article{ Chen2010MolProbityAllAtomStructureValidationForMacromolecularCrystallography,
author = {Chen, Vincent B and Arendall, W Bryan and Headd, Jeffrey J
and Keedy, Daniel A and Immormino, Robert M and Kapral,
Gary J and Murray, Laura W and Richardson, Jane S and
Richardson, David C},
title = {MolProbity: all-atom structure validation for
macromolecular crystallography},
journal = {Acta Crystallographica Section D: Biological
Crystallography},
year = {2010},
volume = {66},
number = {1},
pages = {12--21},
publisher = {International Union of Crystallography}
}
@Article{ Croll2018IsoldeAPhyiscallyRealisticEnvironmentForModelBuildingIntoLowReoslutionElectronDensityMaps,
author = {Tristan Ian Croll},
title = {<i>isolde</i>: a Physically Realistic Environment for
Model Building Into Low-Resolution Electron-Density Maps},
journal = {Acta Crystallographica Section D Structural Biology},
volume = 74,
number = 6,
pages = {519-530},
year = 2018,
doi = {10.1107/s2059798318002425},
url = {http://dx.doi.org/10.1107/S2059798318002425},
date_added = {Sun Jul 21 11:38:17 2024}
}
@Article{ DeZitter2022Xtrapol8EnablesAutomaticElucidationOfLowOccupancyIntermediateStatesInCrystallographicStudies,
author = {De Zitter, Elke and Coquelle, Nicolas and Oeser, Paula and
Barends, Thomas RM and Colletier, Jacques-Philippe},
title = {Xtrapol8 enables automatic elucidation of low-occupancy
intermediate-states in crystallographic studies},
doi = {10.1038/s42003-022-03575-7},
number = {1},
pages = {640},
volume = {5},
file = {:DeZitter2022Xtrapol8EnablesAutomaticElucidationOfLowOccupancyIntermediateStatesInCrystallographicStudies.pdf:PDF},
journal = {Communications Biology},
publisher = {Nature Publishing Group UK London},
year = {2022},
annote = {Elke talked about this paper in the SSRL 2023 Workshp}
}
@Article{ Dolomanov2009OLEX2,
author = {Dolomanov, Oleg V and Bourhis, Luc J and Gildea, Richard J
and Howard, Judith AK and Puschmann, Horst},
title = {OLEX2: a complete structure solution, refinement and
analysis program},
doi = {10.1107/S0021889808042726},
number = {2},
pages = {339--341},
volume = {42},
file = {:Dolomanov2009OLEX2ACompleteStructureSolutionRefinementAndAnalysisProgram.pdf:PDF},
journal = {Journal of Applied Crystallography},
publisher = {International Union of Crystallography},
year = {2009}
}
@Article{ Emsley2010FeaturesAndDevelopmentOfCoot,
author = {Emsley, Paul and Lohkamp, Bernhart and Scott, William G.
and Cowtan, Kevin},
title = {Features and development of Coot},
doi = {10.1107/S0907444910007493},
number = {4},
pages = {486-501},
url = {file:///Users/blaine/0papersLabeled/Emsley2010FeaturesAndDevelopmentOfCoot.pdf},
volume = {66},
abstract = {Coot is a molecular-graphics application for model
building and validation of biological macromolecules. The
program displays electron-density maps and atomic models
and allows model manipulations such as idealization,
real-space refinement, manual rotation/translation,
rigid-body fitting, ligand search, solvation, mutations,
rotamers and Ramachandran idealization. Furthermore, tools
are provided for model validation as well as interfaces to
external programs for refinement, validation and graphics.
The software is designed to be easy to learn for novice
users, which is achieved by ensuring that tools for common
tasks are 'discoverable' through familiar user-interface
elements (menus and toolbars) or by intuitive behaviour
(mouse controls). Recent developments have focused on
providing tools for expert users, with customisable key
bindings, extensions and an extensive scripting interface.
The software is under rapid development, but has already
achieved very widespread use within the crystallographic
community. The current state of the software is presented,
with a description of the facilities available and of some
of the underlying methods employed.},
annote = {This read.},
date_added = {Wed Nov 16 05:04:12 2022},
endnotereftype= {Journal Article},
file = {/Users/blaine/0papersLabeled/Emsley2010FeaturesAndDevelopmentOfCoot.pdf},
journal = {Acta Crystallographica Section D: Biological
Crystallography},
keywords = {'data scaling', 'single-wavelength anomalous dispersion',
'sulfur substructure determination', 'long-wavelength
X-rays', 'soft X-rays', 'native phasing', 'S-SAD', 'de novo
sulfur SAD phasing', 'anomalous diffraction', 'experimental
phasing', 'anomalous signal', SAD, 408, 409, 411, 423, 427,
430, 431, 432, 2093, 2707},
owner = {blaine-mooers},
publisher = {International Union of Crystallography},
shorttitle = {Features and development of Coot},
year = {2010}
}
@Article{ Giacovazzo2019UpdatingDirectMethods,
author = {Carmelo Giacovazzo},
title = {Updating Direct Methods},
journal = {Acta Crystallographica Section A Foundations and
Advances},
volume = 75,
number = 1,
pages = {142-157},
year = 2019,
doi = {10.1107/s2053273318016443},
url = {http://dx.doi.org/10.1107/S2053273318016443},
date_added = {Sat Jul 20 09:28:49 2024},
file = {:Giacovazo2019UpdatingDirectMethods.pdf:PDF}
}
@Article{ Harris2020ArrayProgrammingWithNumpy,
author = {Charles R. Harris and K. Jarrod Millman and St{\'e}fan J.
van der Walt and Ralf Gommers and Pauli Virtanen and David
Cournapeau and Eric Wieser and Julian Taylor and Sebastian
Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
Brett and Allan Haldane and Jaime Fern{\'a}ndez del R{\'i}o
and Mark Wiebe and Pearu Peterson and Pierre
G{\'e}rard-Marchant and Kevin Sheppard and Tyler Reddy and
Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
Travis E. Oliphant},
title = {Array Programming With Numpy},
journal = {Nature},
volume = 585,
number = 7825,
pages = {357-362},
year = 2020,
doi = {10.1038/s41586-020-2649-2},
url = {http://dx.doi.org/10.1038/s41586-020-2649-2},
date_added = {Mon Jul 22 13:35:57 2024},
file = {:Harris2020ArrayProgrammingWithNumpy.pdf:PDF}
}
@Article{ Hunter2007MatplotlibA2DGraphicsEnvironment,
author = {John D. Hunter},
title = {Matplotlib: A 2D Graphics Environment},
doi = {doi.ieeecomputersociety.org/10.1109/MCSE.2007.55},
issn = {1521-9615},
number = {undefined},
pages = {90-95},
volume = {9},
abstract = {Matplotlib is a 2D graphics package used for Python for
application development, interactive scripting, and
publication-quality image generation across user interfaces
and operating systems.},
address = {Los Alamitos, CA, USA},
file = {:Hunter2007MatplotlibA2DGraphicsEnvironment.pdf:PDF},
journal = {Computing in Science \& Engineering},
publisher = {IEEE COMPUTER SOC},
year = {2007}
}
@Article{ Jaynes1957InformationTheoryStatisticalMechanics,
author = {E. T. Jaynes},
title = {Information Theory and Statistical Mechanics},
journal = {Physical Review},
volume = 106,
number = 4,
pages = {620-630},
year = 1957,
doi = {10.1103/physrev.106.620},
url = {http://dx.doi.org/10.1103/PhysRev.106.620},
date_added = {Sun Jul 21 09:15:06 2024}
}
@Misc{ Jmol2024,
author = {Jmol},
title = {Jmol: an open-source Java viewer for chemical structures
in 3D.},
note = {16.2},
url = {http://www.jmol.org/},
creationdate = {2024-07-23T13:54:53}
}
@Article{ Jumper2021HighlyAccurateProteinStructurePredictionWithAlphaFold,
author = {Jumper, John and Evans, Richard and Pritzel, Alexander and
Green, Tim and Figurnov, Michael and Ronneberger, Olaf and
Tunyasuvunakool, Kathryn and Bates, Russ and
{\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
title = {Highly accurate protein structure prediction with
AlphaFold},
doi = {10.1038/s41586-021-03819-2},
number = {7873},
pages = {583--589},
volume = {596},
file = {:Jumper2021HighlyAccurateProteinStructurePredictionWithAlphaFold.pdf:PDF},
journal = {Nature},
publisher = {Nature Publishing Group},
year = {2021}
}
@Article{ Jurrus2018ImprovementsToTheAPBSBiomolecularSolvationSoftwareSuite,
author = {Jurrus, Elizabeth and Engel, Dave and Star, Keith and
Monson, Kyle and Brandi, Juan and Felberg, Lisa E. and
Brookes, David H. and Wilson, Leighton and Chen, Jiahui and
Liles, Karina and Chun, Minju and Li, Peter and Gohara,
David W. and Dolinsky, Todd and Konecny, Robert and Koes,
David R. and Nielsen, Jens Erik and Head-Gordon, Teresa and
Geng, Weihua and Krasny, Robert and Wei, Guo-Wei and Holst,
Michael J. and McCammon, J. Andrew and Baker, Nathan A.},
date = {2018},
journaltitle = {Protein Science},
title = {Improvements to the APBS biomolecular solvation software
suite},
doi = {10.1002/pro.3280},
number = {1},
pages = {112-128},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3280},
volume = {27},
abstract = {Abstract The Adaptive Poisson–Boltzmann Solver (APBS)
software was developed to solve the equations of continuum
electrostatics for large biomolecular assemblages that have
provided impact in the study of a broad range of chemical,
biological, and biomedical applications. APBS addresses the
three key technology challenges for understanding solvation
and electrostatics in biomedical applications: accurate and
efficient models for biomolecular solvation and
electrostatics, robust and scalable software for applying
those theories to biomolecular systems, and mechanisms for
sharing and analyzing biomolecular electrostatics data in
the scientific community. To address new research
applications and advancing computational capabilities, we
have continually updated APBS and its suite of accompanying
software since its release in 2001. In this article, we
discuss the models and capabilities that have recently been
implemented within the APBS software package including a
Poisson–Boltzmann analytical and a semi-analytical
solver, an optimized boundary element solver, a
geometry-based geometric flow solvation model, a graph
theory-based algorithm for determining pKa values, and an
improved web-based visualization tool for viewing
electrostatics.},
annote = {I need to read this.},
creationdate = {2023-05-23T19:30:37},
file = {:Jurrus2018ImprovementsToTheAPBSBiomolecularSolvationSoftwareSuite.pdf:PDF},
keywords = {electrostatics, software, solvation, titration, pKa}
}
@Article{ Kabsch2010XDS,
author = {Kabsch, Wolfgang},
title = {Xds},
doi = {https://doi.org/10.1107/S0907444909047337},
number = {2},
pages = {125--132},
url = {file:///Users/blaine/0papersLabeled/Kabsch2010Xds.pdf},
volume = {66},
abstract = {The usage and control of recent modifications of the
program package XDS for the processing of rotation images
are described in the context of previous versions. New
features include automatic determination of spot size and
reflecting range and recognition and assignment of crystal
symmetry. Moreover, the limitations of earlier package
versions on the number of correction/scaling factors and
the representation of pixel contents have been removed.
Large program parts have been restructured for parallel
processing so that the quality and completeness of
collected data can be assessed soon after measurement.},
annote = {XDS reference.},
date_added = {Wed Nov 16 05:04:12 2022},
file = {/Users/blaine/0papersLabeled/Kabsch2010Xds.pdf},
journal = {Acta Crystallographica Section D: Biological
Crystallography},
keywords = {'data scaling', 'single-wavelength anomalous dispersion',
'sulfur substructure determination', 'long-wavelength
X-rays', 'soft X-rays', 'native phasing', 'S-SAD', 'de novo
sulfur SAD phasing', 'anomalous diffraction', 'experimental
phasing', 'anomalous signal', SAD, 408, 409, 411, 423, 427,
430, 431, 432, 2093, 2707},
publisher = {International Union of Crystallography},
year = {2010}
}
@Article{ Krishna2024GeneralizedBiomolecularModelingAndDesignWithRoseTTAFoldAllAtom,
author = {Krishna, Rohith and Wang, Jue and Ahern, Woody and
Sturmfels, Pascal and Venkatesh, Preetham and Kalvet,
Indrek and Lee, Gyu Rie and Morey-Burrows, Felix S and
Anishchenko, Ivan and Humphreys, Ian R and others},
title = {Generalized biomolecular modeling and design with
RoseTTAFold All-Atom},
number = {6693},
pages = {eadl2528},
volume = {384},
file = {:Krishna2024GeneralizedBiomolecularModelingAndDesignWithRoseTTAFoldAllAtom.pdf:PDF},
journal = {Science},
keywords = {rosettafold, deep-learning, protein structure prediction},
publisher = {American Association for the Advancement of Science},
year = {2024}
}
@Article{ Kumar2019ArviZAUnifiedLibraryForExploratoryAnalysisOfBayesianModelsInPython,
author = {Kumar, Ravin and Carroll, Colin and Hartikainen, Ari and
Martin, Osvaldo},
title = {ArviZ a unified library for exploratory analysis of
Bayesian models in Python},
number = {33},
pages = {1143},
volume = {4},
file = {:Kumar2019ArviZAUnifiedLibraryForExploratoryAnalysisOfBayesianModelsInPython.pdf:PDF},
journal = {Journal of Open Source Software},
year = {2019}
}
@InProceedings{ Lam2015NumbaALLVMBasedPythonJITCompiler,
author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
booktitle = {Proceedings of the Second Workshop on the LLVM Compiler
Infrastructure in HPC},
title = {Numba: A llvm-based python jit compiler},
pages = {1--6},
year = {2015}
}
@InCollection{ Lam2015NumbaALLVMBasedPythonJITCompiler,
author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
booktitle = {{LLVM '15: Proceedings of the Second Workshop on the LLVM
Compiler Infrastructure in HPC}},
title = {{Numba: a LLVM-based Python JIT compiler}},
doi = {10.1145/2833157.2833162},
isbn = {978-1-45034005-2},
pages = {1--6},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
file = {:Lam2015NumbaALLVMBasedPythonJITCompiler.pdf:PDF},
month = nov,
year = {2015}
}
@Article{ Lawson2024OutcomesEmdataresourceCryoEmLigandModelingChallenge,
author = {Catherine L. Lawson and Andriy Kryshtafovych and Grigore
D. Pintilie and Stephen K. Burley and Ji{\v{r}}{\'i}
{\V{C}}ern{\'y} and Vincent B. Chen and Paul Emsley and
Alberto Gobbi and Andrzej Joachimiak and Sigrid Noreng and
Michael G. Prisant and Randy J. Read and Jane S. Richardson
and Alexis L. Rohou and Bohdan Schneider and Benjamin D.
Sellers and Chenghua Shao and Elizabeth Sourial and Chris
I. Williams and Christopher J. Williams and Ying Yang and
Venkat Abbaraju and Pavel V. Afonine and Matthew L. Baker
and Paul S. Bond and Tom L. Blundell and Tom Burnley and
Arthur Campbell and Renzhi Cao and Jianlin Cheng and
Grzegorz Chojnowski and K. D. Cowtan and Frank DiMaio and
Reza Esmaeeli and Nabin Giri and Helmut Grubm{\"u}ller and
Soon Wen Hoh and Jie Hou and Corey F. Hryc and Carola Hunte
and Maxim Igaev and Agnel P. Joseph and Wei-Chun Kao and
Daisuke Kihara and Dilip Kumar and Lijun Lang and Sean Lin
and Sai R. Maddhuri Venkata Subramaniya and Sumit Mittal
and Arup Mondal and Nigel W. Moriarty and Andrew Muenks and
Garib N. Murshudov and Robert A. Nicholls and Mateusz Olek
and Colin M. Palmer and Alberto Perez and Emmi Pohjolainen
and Karunakar R. Pothula and Christopher N. Rowley and
Daipayan Sarkar and Luisa U. Sch{\"a}fer and Christopher J.
Schlicksup and Gunnar F. Schr{\"o}der and Mrinal Shekhar
and Dong Si and Abhishek Singharoy and Oleg V. Sobolev and
Genki Terashi and Andrea C. Vaiana and Sundeep C. Vedithi
and Jacob Verburgt and Xiao Wang and Rangana Warshamanage
and Martyn D. Winn and Simone Weyand and Keitaro Yamashita
and Minglei Zhao and Michael F. Schmid and Helen M. Berman
and Wah Chiu},
title = {Outcomes of the Emdataresource Cryo-Em Ligand Modeling
Challenge},
journal = {Nature Methods},
volume = 21,
number = 7,
pages = {1340-1348},
year = 2024,
doi = {10.1038/s41592-024-02321-7},
url = {http://dx.doi.org/10.1038/s41592-024-02321-7},
date_added = {Mon Jul 22 10:33:57 2024},
file = {:Lawson2024OutcomesEmdataresourceCryoEmLigandModelingChallenge.pdf:PDF}
}
@Article{ Lawson2024TheNucleicAcidKnowledgebaseANewPortalFor3DStructuralInformationAboutNucleicAcids,
author = {Lawson, Catherine L. and Berman, Helen M. and Chen, Li and
Vallat, Brinda and Zirbel, Craig L.},
title = {{The Nucleic Acid Knowledgebase: a new portal for 3D
structural information about nucleic acids}},
doi = {10.1093/nar/gkad957},
issn = {0305-1048},
number = {D1},
pages = {D245--D254},
volume = {52},
file = {:Lawson2024TheNucleicAcidKnowledgebaseANewPortalFor3DStructuralInformationAboutNucleicAcids.pdf:PDF},
journal = {Nucleic Acids Research},
month = jan,
publisher = {Oxford Academic},
year = {2024}
}
@Article{ Liebschner2019RecentDevelopmentsInPhenix,
author = {Liebschner, Dorothee and Afonine, Pavel V and Baker,
Matthew L and Bunk{\'o}czi, G{\'a}bor and Chen, Vincent B
and Croll, Tristan I and Hintze, Bradley and Hung, L-W and
Jain, Swati and McCoy, Airlie J and others},
title = {Macromolecular structure determination using X-rays,
neutrons and electrons: recent developments in Phenix},
doi = {10.1107/S2059798319011471},
number = {10},
pages = {861--877},
volume = {75},
abstract = {Diffraction(X-ray,neutronandelectron)andelectroncryo-microscopyare
powerfulmethodstodeterminethree-dimensionalmacromolecularstructures,
whicharerequiredtounderstandbiologicalprocessesandtodevelopnew
therapeuticsagainstdiseases.Theoverallstructure-solutionworkflowissimilar
forthesetechniques,butnuancesexistbecausethepropertiesofthereduced
experimentaldataaredifferent.Softwaretoolsforstructuredetermination
shouldthereforebetailoredforeachmethod.Phenixisacomprehensive
softwarepackageformacromolecularstructuredeterminationthathandlesdata
fromanyofthesetechniques.TasksperformedwithPhenixincludedata-quality
assessment,mapimprovement,modelbuilding,thevalidation/rebuilding/
refinementcycleanddeposition.Eachtoolcaterstothetypeofexperimental
data.ThedesignofPhenixemphasizestheautomationofprocedures,where
possible,tominimizerepetitiveandtime-consumingmanualtasks,whiledefault
parametersarechosentoencouragebestpractice.Agraphicaluserinterface
providesaccesstomanycommand-linefeaturesofPhenixandstreamlinesthe
transitionbetweenprograms,projecttrackingandre-runningofprevioustasks.},
annote = {This is the paper the one to cite for Phenix.},
file = {:Liebschner2019MacromolecularStructureDeterminationUsingXRaysNeutronsAndElectronsRecentDevelopmentsInPhenix.pdf:PDF},
journal = {Acta Crystallographica Section D: Structural Biology},
publisher = {International Union of Crystallography},
year = {2019}
}
@Article{ Lu2015DSSRAnIntegratedSoftwareToolForDissectingTheSpatialStruturesOfRNA,
author = {Lu, Xiang-Jun and Bussemaker, Harmen J and Olson, Wilma
K},
title = {DSSR: an integrated software tool for dissecting the
spatial structure of RNA},
doi = {10.1093/nar/gkv716},
number = {21},
pages = {e142--e142},
volume = {43},
file = {:Lu2015DSSRAnIntegratedSoftwareToolForDissectingTheSpatialStruturesOfRNA.pdf:PDF},
journal = {Nucleic Acids Research},
publisher = {Oxford University Press},
year = {2015}
}
@Article{ Matthews1968SolventContentOfProteinCrystals,
author = {Matthews, Brian W},
title = {Solvent content of protein crystals},
number = {2},
pages = {491--497},
volume = {33},
file = {:Matthews1968SolventContentOfProteinCrystals.pdf:PDF},
journal = {Journal of molecular biology},
publisher = {Elsevier},
year = {1968}
}
@InProceedings{ Mckinney2010DataStructuresStatisticalComputingPython,
author = {Wes McKinney},
title = {Data Structures for Statistical Computing in Python},
booktitle = {Proceedings of the Python in Science Conference},
year = 2010,
pages = {nil},
doi = {10.25080/majora-92bf1922-00a},
url = {http://dx.doi.org/10.25080/Majora-92bf1922-00a},
date_added = {Mon Jul 22 13:26:16 2024},
month = {-},
file = {:Mckinney2010DataStructuresStatisticalComputingPython.pdf:PDF}
}
@InProceedings{ Mckinney2010DataStructuresStatisticalComputingPython,
author = {Wes McKinney},
title = {Data Structures for Statistical Computing in Python},
booktitle = {Proceedings of the Python in Science Conference},
year = 2010,
pages = {56-61},
doi = {10.25080/majora-92bf1922-00a},
url = {http://dx.doi.org/10.25080/Majora-92bf1922-00a},
date_added = {Mon Jul 22 13:26:16 2024},
month = {July},
file = {:Mckinney2010DataStructuresStatisticalComputingPython.pdf:PDF}
}
@Article{ Meng2023UCSFChimeraXToolsForStructureBuildingAndAnalysis,
author = {Meng, Elaine C. and Goddard, Thomas D. and Pettersen, Eric
F. and Couch, Greg S. and Pearson, Zach J. and Morris, John
H. and Ferrin, Thomas E.},
title = {UCSF ChimeraX: Tools for Structure Building and Analysis},
doi = {https://doi.org/10.1002/pro.4792},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.4792},
note = {e4792 PRO-23-0359.R1},
number = {n/a},
pages = {e4792},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4792},
volume = {n/a},
abstract = {Abstract Advances in computational tools for atomic model
building are leading to accurate models of large molecular
assemblies seen in electron microscopy, often at
challenging resolutions of 3-4 Å. We describe new methods
in the UCSF ChimeraX molecular modeling package that take
advantage of machine-learning structure predictions,
provide likelihood-based fitting in maps, and compute
per-residue scores to identify modeling errors. Additional
model-building tools assist analysis of mutations,
post-translational modifications, and interactions with
ligands. We present the latest ChimeraX model-building
capabilities, including several community-developed
extensions. ChimeraX is available free of charge for
noncommercial use at https://www.rbvi.ucsf.edu/chimerax.
This article is protected by copyright. All rights
reserved.},
file = {:MengUCSFChimeraXToolsForStructureBuildingAndAnalysis.pdf:PDF},
journal = {Protein Science},
keywords = {ChimeraX, atomic model building, cryo-electron microscopy,
AlphaFold, protein structure prediction, refinement}
}
@Article{ Minor2006HKL3000TheIntegrationOfDataReductionAndStructureSolutionFromDiffractionImagesToAnInitialModelInMinutes,
author = {Minor, W. and Cymborowski, M. and Otwinowski, Z. and
Chruszcz, M.},
title = {{HKL-3000: the integration of data reduction and structure
solution {\textendash} from diffraction images to an
initial model in minutes}},
doi = {10.1107/S0907444906019949},
issn = {0907-4449},
number = {8},
pages = {859--866},
volume = {62},
file = {:Minor2006HKL3000TheIntegrationOfDataReductionAndStructureSolutionFromDiffractionImagesToAnInitialModelInMinutes.pdf:PDF},
journal = {Acta Crystallogr., Sect. D: Biol. Crystallogr.},
month = aug,
publisher = {International Union of Crystallography},
year = {2006}
}
@Article{ Mirdita2022ColabFoldMakingProteinFoldingAccessibleToAll,
author = {Mirdita, Milot and Sch{\"u}tze, Konstantin and Moriwaki,
Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and
Steinegger, Martin},
title = {ColabFold: making protein folding accessible to all},
doi = {10.1038/s41592-022-01488-1},
pages = {1--4},
file = {:Mirdita2022ColabFoldMakingProteinFoldingAccessibleToAll.pdf:PDF},
journal = {Nature Methods},
publisher = {Nature Publishing Group},
year = {2022}
}
@Article{ Morris2004OnTheInterpretationAndUseEsquaredProfiles,
author = {Richard J. Morris and Eric Blanc and G{\'e}rard Bricogne},
title = {On the Interpretation and Use of
〈|<i>E</i>|<sup>2</sup>〉(<i>d</i>*) Profiles},
journal = {Acta Crystallographica Section D Biological
Crystallography},
volume = 60,
number = 2,
pages = {227-240},
year = 2004,
doi = {10.1107/s0907444903025538},
url = {http://dx.doi.org/10.1107/S0907444903025538},
date_added = {Sat Jul 20 09:05:02 2024},
file = {:Morris2004OnTheInterpretationAndUseEsquaredProfiles.pdf:PDF}
}
@Article{ Murshudov2011Refmac5ForTheRefinementMacromolecularCrystalStructures,
author = {Garib N. Murshudov and Pavol Skub{\'a}k and Andrey A.
Lebedev and Navraj S. Pannu and Roberto A. Steiner and
Robert A. Nicholls and Martyn D. Winn and Fei Long and
Alexei A. Vagin},
title = {<i>refmac</i>5 for the Refinement of Macromolecular
Crystal Structures},
journal = {Acta Crystallographica Section D Biological
Crystallography},
volume = 67,
number = 4,
pages = {355-367},
year = 2011,
doi = {10.1107/s0907444911001314},
url = {http://dx.doi.org/10.1107/S0907444911001314},
date_added = {Mon Jul 22 17:10:55 2024},
file = {:Murshudov2011Refmac5ForTheRefinementMacromolecularCrystalStructures.pdf:PDF}
}
@Article{ Painter2006ServerGenerationMultiGroupTlsModels,
author = {Jay Painter and Ethan A. Merritt},
title = {<i>tlsmd</i>web Server for the Generation of Multi-Group
Tls Models},
journal = {Journal of Applied Crystallography},
volume = 39,
number = 1,
pages = {109-111},
year = 2006,
doi = {10.1107/s0021889805038987},
url = {http://dx.doi.org/10.1107/S0021889805038987},
date_added = {Sat Jul 20 13:39:46 2024},
file = {:Painter2006ServerGenerationMultiGroupTLSModels.pdf:PDF}
}
@Article{ Pape2004HKL2MAPAGraphicalUserInterfaceForMacromolecularPhasingWithSHELXPrograms,
author = {Pape, Thomas and Schneider, Thomas R},
title = {HKL2MAP: a graphical user interface for macromolecular
phasing with SHELX programs},
doi = {https://doi.org/10.1107/S0021889804018047},
number = {5},
pages = {843--844},
url = {file:///Users/blaine/0papersLabeled/Pape2004HKL2MAPAGraphicalUserInterfaceForMacromolecularPhasingWithSHELXPrograms.pdf},
volume = {37},
abstract = {One approach to phasing of macromolecular crystal
structure is to exploit the small changes in diffracted
intensities induced by the inclusion of heavy atoms, to
alter the wavelength in the presence of anomalous
scatterers, or to use a combination thereof. \\ \\ In the
SHELX suite of crystallographic programs, the computations
involved in the respective phasing procedures are divided
into three steps: (i) extraction of structure factors
representing the substructure of heavy atoms and/or
anomalous scatterers only (SHELXC; Sheldrick,
2004[Sheldrick, G. M. (2004). SHELXC, University of
Göttingen, Germany.]), (ii) determination of the
substructure (SHELXD; Schneider & Sheldrick,
2002[Schneider, T. R. & Sheldrick, G. M. (2002). Acta
Cryst. D58, 1772-1779.]), (iii) calculation of initial
phases based on the knowledge of the substructure and
improvement of these phases by density modification
(SHELXE; Sheldrick, 2002[Sheldrick, G. M. (2002). Z.
Kristallogr. 217, 644-650.]). \\ \\ A number of crystal
structures have been solved using the combination of the
programs mentioned above. However, in particular for the
inexperienced user, the creation of correct input files and
the interpretation of the intermediate results can be a
major obstacle. To simplify the use of the SHELX programs
for phasing and as a teaching tool, we have developed a
graphical user interface, HKL2MAP.},
annote = {This read. There is a webpage for this software
\url{http://webapps.embl-hamburg.de/hkl2map/}.},
date_added = {Wed Nov 02 05:04:12 2022},
file = {/Users/blaine/0papersLabeled/Pape2004HKL2MAPAGraphicalUserInterfaceForMacromolecularPhasingWithSHELXPrograms.pdf},
journal = {Journal of applied crystallography},
keywords = {'multiple-wavelength anomalous diffraction (MAD) phasing',
'single-wavelength anomalous diffraction (SAD) phasing',
'computer programs', 'native phasing', 'anomalous
diffraction', 'experimental phasing', 'anomalous signal',
SAD, 408, 409, 411, 423, 427, 430, 431, 432, 2093, 2707},
publisher = {International Union of Crystallography},
year = {2004}
}
@Article{ Salvatier2016ProbabilisticProgrammingInPythonUsingPyMC3,
author = {Salvatier, John and Wiecki, Thomas V and Fonnesbeck,
Christopher},
title = {Probabilistic programming in Python using PyMC3},
pages = {e55},
volume = {2},
file = {:Salvatier2016ProbabilisticProgrammingInPythonUsingPyMC3.pdf:PDF},
journal = {PeerJ Computer Science},
publisher = {PeerJ Inc.},
year = {2016}
}
@InProceedings{ Seabold2010Statsmodels,
author = {Skipper Seabold and Josef Perktold},
title = {Statsmodels: Econometric and Statistical Modeling with
Python},
booktitle = {Proceedings of the Python in Science Conference},
year = 2010,
pages = {nil},
doi = {10.25080/majora-92bf1922-011},
url = {http://dx.doi.org/10.25080/Majora-92bf1922-011},
date_added = {Mon Jul 22 13:28:58 2024},
month = {-},
file = {:Seabold2010Statsmodels.pdf:PDF}
}
@Article{ Sheldrick2008AShortHistoryOfSHELX,
author = {Sheldrick, George M.},
title = {A short history of {S}{H}{E}{L}{X}},
doi = {10.1107/S0108767307043930},
number = {1},
pages = {112--122},
url = {https://doi.org/10.1107/S0108767307043930},
volume = {64},
abstract = {An account is given of the development of the {\it SHELX}
system of computer programs from {\it SHELX}-76 to the
present day. In addition to identifying useful innovations
that have come into general use through their
implementation in {\it SHELX}, a critical analysis is
presented of the less-successful features, missed
opportunities and desirable improvements for future
releases of the software. An attempt is made to understand
how a program originally designed for photographic
intensity data, punched cards and computers over 10000
times slower than an average modern personal computer has
managed to survive for~so~long. {\it SHELXL} is the most
widely used program for small-molecule refinement and {\it
SHELXS} and {\it SHELXD} are often employed for structure
solution despite the availability of objectively superior
programs. {\it SHELXL} also finds a niche for the
refinement of macromolecules against high-resolution or
twinned data; {\it SHELXPRO} acts as an interface for
macromolecular applications. {\it SHELXC}, {\it SHELXD} and
{\it SHELXE} are proving useful for the experimental
phasing of macromolecules, especially because they are fast
and robust and so are often employed in pipelines for {\it
high-throughput} phasing. This paper could serve as a
general literature citation when one or more of the
open-source {\it SHELX} programs (and the Bruker AXS
version {\it SHELXTL}) are employed in the course of a
crystal-structure determination.},
file = {:Sheldrick2008AShortHistoryOfSHELX.pdf:PDF},
journal = {Acta Crystallographica Section A},
keywords = {computer programs, crystal structure determination,
phasing, SHELX, structure refinement},
month = {Jan},
year = {2008}
}
@Article{ Sheldrick2010ExperimentalPhasingWithSHELXCDECombiningChainTracingWithDensityModification,
author = {Sheldrick, George M.},
title = {Experimental phasing with SHELXC/D/E: combining chain
tracing with density modification},
doi = {https://doi.org/10.1107/S0907444909038360},
note = {1399-0047 (Electronic) 0907-4449 (Linking)},
number = {Pt 4},
pages = {479-85},
url = {http://dx.doi.org/10.1107/S0907444909038360},
volume = {66},
abstract = {The programs SHELXC, SHELXD and SHELXE are designed to
provide simple, robust and efficient experimental phasing
of macromolecules by the SAD, MAD, SIR, SIRAS and RIP
methods and are particularly suitable for use in automated
structure-solution pipelines. This paper gives a general
account of experimental phasing using these programs and
describes the extension of iterative density modification
in SHELXE by the inclusion of automated protein main-chain
tracing. This gives a good indication as to whether the
structure has been solved and enables interpretable maps to
be obtained from poorer starting phases. The autotracing
algorithm starts with the location of possible
seven-residue [alpha]-helices and common tripeptides.
After extension of these fragments in both directions,
various criteria are used to decide whether to accept or
reject the resulting poly-Ala traces. Noncrystallographic
symmetry (NCS) is applied to the traced fragments, not to
the density. Further features are the use of a `no-go' map
to prevent the traces from passing through heavy atoms or
symmetry elements and a splicing technique to combine the
best parts of traces (including those generated by NCS)
that partly overlap.},
annote = {This read.},
date_added = {Wed Nov 16 05:04:12 2022},
endnotereftype= {Journal Article},
file = {/Users/blaine/0papersLabeled/Sheldrick2010ExperimentalPhasingWithSHELXCDECombiningChainTracingWithDensityModification.pdf},
journal = {Acta Crystallogr D Biol Crystallogr},
keywords = {'data scaling', 'single-wavelength anomalous dispersion',
'sulfur substructure determination', 'long-wavelength
X-rays', 'soft X-rays', 'native phasing', 'S-SAD', 'de novo
sulfur SAD phasing', 'anomalous diffraction', 'experimental
phasing', 'anomalous signal', SAD, 408, 409, 411, 423, 427,
430, 431, 432, 2093, 2707},
owner = {blaine-mooers},
shorttitle = {Experimental phasing with SHELXC/D/E: combining chain
tracing with density modification},
year = {2010}
}
@Article{ Sheldrick2015CrystalStructureRefinementWithSHELXL,
author = {George M. Sheldrick},
title = {Crystal Structure Refinement With<i>shelxl</i>},
journal = {Acta Crystallographica Section C Structural Chemistry},
volume = 71,
number = 1,
pages = {3-8},
year = 2015,
doi = {10.1107/s2053229614024218},
url = {http://dx.doi.org/10.1107/S2053229614024218},
date_added = {Sat Jul 20 12:31:24 2024},
file = {:/Users/blaine/0papersLabeled/Sheldrick2015CrystalStructureRefinementWithSHELXL.pdf}
}
@Article{ Sheldrick2015CrystalStructureRefinementWithSHELXL,
author = {Sheldrick, George M},
title = {Crystal structure refinement with SHELXL},
number = {1},
pages = {3--8},
volume = {71},
annote = {This paper has a zillion citations.},
file = {:Sheldrick2015CrystalStructureRefinementWithSHELXL.pdf:PDF},
journal = {Acta Crystallographica Section C: Structural Chemistry},
publisher = {International Union of Crystallography},
year = {2015}
}
@Article{ Smart2012ExploitingStructureSimilarityRefinementAutomatedNCSandTargetStructureRestraintsInBuster,
author = {Oliver S. Smart and Thomas O. Womack and Claus Flensburg
and Peter Keller and Włodek Paciorek and Andrew Sharff and
Clemens Vonrhein and G{\'e}rard Bricogne},
title = {Exploiting Structure Similarity in Refinement: Automated
NCS and Target-Structure Restraints In<i>buster</i>},
journal = {Acta Crystallographica Section D Biological
Crystallography},
volume = 68,
number = 4,
pages = {368-380},
year = 2012,
doi = {10.1107/s0907444911056058},
url = {http://dx.doi.org/10.1107/S0907444911056058},
date_added = {Mon Jul 22 16:57:54 2024},
file = {:Smart2012ExploitingStructureSimilarityRefinementAutomatedNCSandTargetStructureRestraintsInBuster.pdf:PDF}
}
@Article{ Tarini2006AmbientOcclusionAndEdgeCueingForEnhancingRealTimeMolecularVisualization,
author = {Tarini, Marco and Cignoni, Paolo and Montani, Claudio},
title = {Ambient occlusion and edge cueing for enhancing real time
molecular visualization},
doi = {10.1109/tvcg.2006.115},
number = {5},
pages = {1237--1244},
volume = {12},
file = {:Tarini2006AmbientOcclusionAndEdgeCueingForEnhancingRealTimeMolecularVisualization.pdf:PDF},
journal = {IEEE Trans Vis Comput Graphics},
publisher = {IEEE},
year = {2006}
}
@Article{ Tronrud1987AnEfficientGeneralPurposeLeastSquaresRefinementProgramForMacromolecularStructures,
author = {Tronrud, D. E. Ten Eyck L. F. and Matthews, B. W.},
title = {An Efficient General-Purpose Least-Squares Refinement
Program for Macromolecular Structures},
journal = {Acta Cryst.},
year = {1987},
volume = {A43},
pages = {489-501},
endnotereftype= {Journal Article},
owner = {blaine-mooers},
shorttitle = {An Efficient General-Purpose Least-Squares Refinement
Program for Macromolecular Structures}
}
@Article{ Virtanen2020SciPy10FundamentalAlgorithmsForScientificComputingInPython,
author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E.
and Haberland, Matt and Reddy, Tyler and Cournapeau, David
and Burovski, Evgeni and Peterson, Pearu and Weckesser,
Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan
J. and Brett, Matthew and Wilson, Joshua and Millman, K.
Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and
Jones, Eric and Kern, Robert and Larson, Eric and Carey, C
J and Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
{VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef
and Cimrman, Robert and Henriksen, Ian and Quintero, E. A.