Ecosyste.ms: Papers

10.1107/S2059798318003455

Recent developments in<i>MrBUMP</i>: better search-model preparation, graphical interaction with search models, and solution improvement and assessment
Cited by: 34
Author(s): Ronan Keegan, Stuart McNicholas, Jens M. H. Thomas, Adam J Simpkin, Felix Šimkovic, Ville Uski, Charles Ballard, Martyn Winn, K.S. Wilson, Daniel J. Rigden
Software Mentions: 5
Published: over 6 years ago

10.1107/S0907444913022750

<i>Phaser.MRage</i>: automated molecular replacement
Cited by: 204
Author(s): G. Bunkóczi, Nathaniel Echols, Airlie J. McCoy, Robert D. Oeffner, Paul D. Adams, Randy J. Read
Software Mentions: 5
Published: about 11 years ago

10.1016/j.jmb.2018.06.007

The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil
Cited by: 10
Author(s): Sarah L. Rouse, Fisentzos Stylianou, Howie Wu, Jamie-Lee Berry, Lee Sewell, Rhodri M. L. Morgan, Andrea C. Sauerwein, Steve Matthews
Software Mentions: 4
Published: about 6 years ago

10.1107/S2059798317017582

<i>ARCIMBOLDO</i>on coiled coils
Cited by: 39
Author(s): Iracema Caballero, Massimo Sammito, Claudia Millán, А. А. Лебедев, Nicolas Soler, Isabel Usón
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798318002310

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in<i>AMPLE</i>
Cited by: 14
Author(s): Daniel J. Rigden, Jens M. H. Thomas, Felix Šimkovic, Adam J Simpkin, Martyn Winn, Olga Mayans, Ronan Keegan
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798319015730

Factors influencing estimates of coordinate error for molecular replacement
Cited by: 6
Author(s): Kaushik Hatti, Airlie J. McCoy, Robert D. Oeffner, Massimo Sammito, Randy J. Read
Software Mentions: 3
Published: almost 5 years ago

10.1107/S2059798320000443

Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modelling
Cited by: 7
Author(s): Jens M. H. Thomas, Ronan Keegan, Daniel J. Rigden, Owen R. Davies
Software Mentions: 3
Published: over 4 years ago

10.1107/S2059798320001679

<i>ALEPH</i>: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
Cited by: 15
Author(s): Ana María Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo Sammito
Software Mentions: 3
Published: over 4 years ago

10.1107/S205979832000056X

<i>ALIXE</i>: a phase-combination tool for fragment-based molecular replacement
Cited by: 14
Author(s): Claudia Millán, Elisabet Jiménez, Antonia Schuster, Kay Diederichs, Isabel Usón
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798318005752

<i>SIMBAD</i>: a sequence-independent molecular-replacement pipeline
Cited by: 24
Author(s): Adam J Simpkin, Felix Šimkovic, Jens M. H. Thomas, Martin Savko, А. А. Лебедев, Ville Uski, Clive Ballard, Marcin Wojdyr, Rui Wu, Ruslan Sanishvili, Yibin Xu, María‐Natalia Lisa, Alejandro Buschiazzo, William Shepard, Daniel J. Rigden, Ronan Keegan
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-71635-1

Small-scale volcanic aerosols variability, processes and direct radiative impact at Mount Etna during the EPL-RADIO campaigns
Cited by: 12
Author(s): Pasquale Sellitto, Giuseppe Salerno, Alessandro La Spina, Tommaso Caltabiano, Simona Scollo, Antonella Boselli, G. Leto, Ricardo Zanmar Sánchez, S. Crumeyrolle, Benjamin Hanoune, Pierre Briole
Software Mentions: 2
Published: about 4 years ago

10.1107/S2059798318004357

On the application of the expected log-likelihood gain to decision making in molecular replacement
Cited by: 35
Author(s): Robert D. Oeffner, Pavel V. Afonine, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read, Airlie J. McCoy
Software Mentions: 2
Published: over 6 years ago

10.1107/S2059798320000467

A practical overview of molecular replacement: <i>Clostridioides difficile</i> PilA1, a difficult case study
Cited by: 3
Author(s): Adam Crawshaw, Arnaud Baslé, Paula S. Salgado
Software Mentions: 2
Published: over 4 years ago

10.1107/S2052252515002080

Routine phasing of coiled-coil protein crystal structures with<i>AMPLE</i>
Cited by: 24
Author(s): Jens M. H. Thomas, Ronan Keegan, Jaclyn Bibby, Martyn Winn, Olga Mayans, Daniel J. Rigden
Software Mentions: 2
Published: over 9 years ago

10.1107/S2052252515003486

Solving coiled-coil protein structures
Cited by: 8
Author(s): Zbigniew Dauter
Software Mentions: 2
Published: over 9 years ago

10.1107/S2052252514024117

Macromolecular<i>ab initio</i>phasing enforcing secondary and tertiary structure
Cited by: 44
Author(s): Claudia Millán, Massimo Sammito, Isabel Usón
Software Mentions: 2
Published: almost 10 years ago

10.1107/S0907444913018453

Application of the<i>AMPLE</i>cluster-and-truncate approach to NMR structures for molecular replacement
Cited by: 13
Author(s): Jaclyn Bibby, Ronan Keegan, Olga Mayans, Martyn Winn, Daniel J. Rigden
Software Mentions: 2
Published: about 11 years ago

10.1107/S2059798320008049

Fragment-based determination of a proteinase K structure from MicroED data using <i>ARCIMBOLDO_SHREDDER</i>
Cited by: 12
Author(s): Logan S. Richards, Claudia Millán, Jennifer Miao, Michael W. Martynowycz, M.R. Sawaya, Tamir Gonen, Rafael J. Borges, Isabel Usón, José A. Rodríguez
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798320000339

<i>SEQUENCE SLIDER</i>: expanding polyalanine fragments for phasing with multiple side-chain hypotheses
Cited by: 8
Author(s): Rafael J. Borges, Kathrin Meindl, Josep Triviño, Massimo Sammito, Ana María Medina, Claudia Millán, Martín Alcorlo, J.A. Hermoso, Marcos R.M. Fontes, Isabel Usón
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798318002292

<i>Fragon</i>: rapid high-resolution structure determination from ideal protein fragments
Cited by: 23
Author(s): Huw T. Jenkins
Software Mentions: 2
Published: over 6 years ago

10.1107/S0907444913027534

Extending molecular-replacement solutions with<i>SHELXE</i>
Cited by: 80
Author(s): Andrea Thorn, George M. Sheldrick
Software Mentions: 2
Published: about 11 years ago

10.1107/S2059798318001365

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination
Cited by: 25
Author(s): Claudia Millán, Massimo Sammito, Airlie J. McCoy, Andrey Fabricio Ziem Nascimento, Giovanna Petrillo, Robert D. Oeffner, T. Dominguez-Gil, J.A. Hermoso, Randy J. Read, Isabel Usón
Software Mentions: 2
Published: over 6 years ago

10.1107/S2059798316000401

An overview of heavy-atom derivatization of protein crystals
Cited by: 40
Author(s): A.C.W. Pike, Elspeth F. Garman, T. Krojer, Frank von Delft, E.P. Carpenter
Software Mentions: 2
Published: over 8 years ago

10.1107/S205979832001133X

Helical ensembles outperform ideal helices in molecular replacement
Cited by: 2
Author(s): Filomeno Sánchez Rodríguez, Adam J Simpkin, Owen R. Davies, Ronan Keegan, Daniel J. Rigden
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0251459

Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc
Cited by: 5
Author(s): Erik I. Hallin, Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda, Clive R. Bramham, Petri Kursula
Software Mentions: 2
Published: over 3 years ago

10.1107/S2059798317015121

An introduction to experimental phasing of macromolecules illustrated by<i>SHELX</i>; new autotracing features
Cited by: 122
Author(s): Isabel Usón, George M. Sheldrick
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnhum.2012.00245

Adaptive thresholding for reliable topological inference in single subject fMRI analysis
Cited by: 40
Author(s): Krzysztof J. Gorgolewski, Amos Storkey, Mark E. Bastin, Cyril Pernet
Software Mentions: 2
Published: almost 13 years ago

10.3389/fmicb.2020.605705

Discovery of an Antibiotic-Related Small Protein of Biocontrol Strain Pseudomonas sp. Os17 by a Genome-Mining Strategy
Cited by: 1
Author(s): Kasumi Takeuchi, Wataru Tsuchiya, Zui Fujimoto, Kosumi Yamada, Nobutaka Someya, Toshimasa Yamazaki
Software Mentions: 2
Published: almost 4 years ago

10.36469/jheor.2021.23684

Persistence with Early-Line Abatacept versus Tumor Necrosis Factor-Inhibitors for Rheumatoid Arthritis Complicated by Poor Prognostic Factors
Cited by: 1
Author(s): Xue Han, Francis Lobo, Michael S. Broder, Eunice Chang, Sarah N Gibbs, David Ridley, Irina Yermilov
Software Mentions: 1
Published: over 3 years ago

10.1098/rsob.210060

Structural basis for the coiled-coil architecture of human CtIP
Cited by: 6
Author(s): Chris Morton, Neil J. Rzechorzek, Joseph D. Maman, Masahiro Kawamura, Hiroshi Sekiguchi, Robert P. Rambo, Yuji Sasaki, Owen R. Davies, Luca Pellegrini
Software Mentions: 1
Published: over 3 years ago

10.1107/S1399004714025784

Exploring the speed and performance of molecular replacement with<i>AMPLE</i>using<i>QUARK ab initio</i>protein models
Cited by: 26
Author(s): Ronan Keegan, Jaclyn Bibby, Jens M. H. Thomas, Dong Xu, Yang Zhang, Olga Mayans, Martyn Winn, Daniel J. Rigden
Software Mentions: 1
Published: almost 10 years ago

10.1107/S0907444913027352

Molecular replacements
Cited by: 2
Author(s): Clive Ballard, Pietro Roversi, Helen Walden
Software Mentions: 1
Published: about 11 years ago

10.1107/S2059798317017557

From crystal to structure with <i>CCP</i>4
Cited by: 21
Author(s): Michael A. Hough, K.S. Wilson
Software Mentions: 1
Published: almost 7 years ago

10.1107/S2059798317014565

Distributed computing for macromolecular crystallography
Cited by: 53
Author(s): Eugene Krissinel, Ville Uski, А. А. Лебедев, Martyn Winn, Charles Ballard
Software Mentions: 1
Published: almost 7 years ago

10.1107/S2059798321004368

Introduction to molecular replacement: a time perspective
Cited by: 4
Author(s): E.J. Dodson
Software Mentions: 1
Published: over 3 years ago

10.1107/S2059798317016436

Approaches to<i>ab initio</i>molecular replacement of α-helical transmembrane proteins
Cited by: 5
Author(s): Jens M. H. Thomas, Felix Šimkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J. Rigden
Software Mentions: 1
Published: almost 7 years ago

10.1107/S2059798319013962

Molecular replacement using structure predictions from databases
Cited by: 14
Author(s): Adam J Simpkin, Jens M. H. Thomas, Felix Šimkovic, Ronan Keegan, Daniel J. Rigden
Software Mentions: 1
Published: about 5 years ago

10.1107/S2059798319015031

Using Phaser and ensembles to improve the performance of SIMBAD
Cited by: 6
Author(s): Adam J Simpkin, Felix Šimkovic, Jens M. H. Thomas, Martin Savko, А. А. Лебедев, Ville Uski, Charles Ballard, Marcin Wojdyr, William Shepard, Daniel J. Rigden, Ronan Keegan
Software Mentions: 1
Published: almost 5 years ago

10.1107/S2059798320014746

<i>Phasertng</i>: directed acyclic graphs for crystallographic phasing
Cited by: 11
Author(s): Airlie J. McCoy, Duncan H. Stockwell, Massimo Sammito, Robert D. Oeffner, Kaushik Hatti, Tristan I. Croll, Randy J. Read
Software Mentions: 1
Published: almost 4 years ago

10.1007/s40629-020-00158-y

Guideline (S2k) on acute therapy and management of anaphylaxis: 2021 update
Cited by: 66
Author(s): Johannes Ring, Kirsten Beyer, Tilo Biedermann, Andreas J. Bircher, Matthias Fischer, Thomas Fuchs, Axel R. Heller, Florian Hoffmann, Isidor Huttegger, Thilo Jakob, Ludger Klimek, Matthias Kopp, Claudia Kugler, Lars Lange, Oliver Pfaar, Ernst Rietschel, Franziska Ruëff, Sabine Schnadt, Roland Seifert, Britta Stöcker, Regina Treudler, Christian Vogelberg, Thomas Werfel, Margitta Worm, H. Sitter, Knut Brockow
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13075-021-02607-7

HLA-DRB1 risk alleles for RA are associated with differential clinical responsiveness to abatacept and adalimumab: data from a head-to-head, randomized, single-blind study in autoantibody-positive early RA
Cited by: 11
Author(s): William F.C. Rigby, Jane H. Buckner, S. Louis Bridges, Marleen Nys, Sheng Gao, Martin S. Polinsky, Neelanjana Ray, Vivian P. Bykerk
Software Mentions: 1
Published: about 3 years ago

10.1002/art.37711

Head‐to‐head comparison of subcutaneous abatacept versus adalimumab for rheumatoid arthritis: Findings of a phase IIIb, multinational, prospective, randomized study
Cited by: 222
Author(s): Michael E. Weinblatt, Michael Schiff, R. Valente, Desirée van der Heijde, Gustavo Citera, Cathy Zhao, Michael A. Maldonado, Roy Fleischmann
Software Mentions: 1
Published: almost 12 years ago

10.1186/s41927-020-00130-x

The pharmacological and clinical aspects behind dose loading of biological disease modifying anti-rheumatic drugs (bDMARDs) in auto-immune rheumatic diseases (AIRDs): rationale and systematic narrative review of clinical evidence
Cited by: 5
Author(s): Gerlienke E. Geurts-Voerman, Lise M Verhoef, Bart J F van den Bemt, Alfons A den Broeder
Software Mentions: 1
Published: over 4 years ago

10.1002/brb3.1617

Optimizing data processing to improve the reproducibility of single‐subject functional magnetic resonance imaging
Cited by: 2
Author(s): David A. Soltysik
Software Mentions: 1
Published: over 4 years ago

10.1186/s40779-018-0152-y

Expert consensus on the evaluation and diagnosis of combat injuries of the Chinese People’s Liberation Army
Cited by: 5
Author(s): Zhaowen Zong, Lianyang Zhang, Hao Qin, Sixu Chen, Lin Zhang, Lei Yang, Xiao-Xue Li, Quanwei Bao, Daocheng Liu, Sihao He, Ya Shen, Rong Zhang, Yuhai Zhao, Xiaozheng Zhong
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.molcel.2019.02.030

Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity
Cited by: 43
Author(s): Malte Gersch, Jane L. Wagstaff, A.V. Toms, Bradford Graves, Stefan Freund, David Komander
Software Mentions: 1
Published: over 5 years ago

10.1016/j.molcel.2016.08.001

SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling
Cited by: 126
Author(s): P.R. Elliott, Derek Leske, Matouš Hrdinka, Katrin Bagola, Berthe Katrine Fiil, Stephen H. McLaughlin, Jane L. Wagstaff, Norbert Volkmar, John C. Christianson, Benedikt M. Kessler, Stefan Freund, David Komander, Mads Gyrd‐Hansen
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0098860

Preoperative Mapping of the Sensorimotor Cortex: Comparative Assessment of Task-Based and Resting-State fMRI
Cited by: 80
Author(s): Cristina Rosazza, Domenico Aquino, Ludovico D’Incerti, Roberto Cordella, Adrian Andronache, Domenico Zacà, Maria Grazia Bruzzone, Giovanni Tringali, Ludovico Minati
Software Mentions: 1
Published: over 10 years ago

10.3390/jcm9062017

Background Glucocorticoid Therapy Has No Impact on Efficacy and Safety of Abatacept or Adalimumab in Patients with Rheumatoid Arthritis
Cited by: 0
Author(s): Yannick Degboé, Michael Schiff, Michael E. Weinblatt, Roy Fleischmann, Harris Ahmad, Arnaud Constantin
Software Mentions: 1
Published: over 4 years ago

10.1007/s00296-017-3739-9

Cost per response for abatacept versus adalimumab in rheumatoid arthritis by ACPA subgroups in Germany, Italy, Spain, US and Canada
Cited by: 10
Author(s): L. Weijers, Christoph Baerwald, Francesco Saverio Mennini, José Manuel Rodríguez-Heredia, Martin Bergman, D. Choquette, K Herrmann, Giulia Attinà, Carmela Nappi, Silvia Jiménez Merino, Chad Patel, Mondher Mtibaa, Jason Foo
Software Mentions: 1
Published: over 7 years ago

10.1186/s13049-015-0113-3

A tailored e-learning program to improve handover in the chain of emergency care: a pre-test post-test study
Cited by: 18
Author(s): Remco Ebben, P.M. van Grunsven, Marie Louise Moors, Peter Aldenhoven, Jordan de Vaan, Roger van Hout, Theo van Achterberg, Lilian Vloet
Software Mentions: 1
Published: over 9 years ago

10.1186/s13049-018-0545-7

The satisfaction regarding handovers between ambulance and emergency department nurses: an observational study
Cited by: 13
Author(s): Gijs Thomas Hovenkamp, Tycho J Olgers, Remco Robert Wortel, Milou Noltes, Bert Dercksen, Jan C. ter Maaten
Software Mentions: 1
Published: about 6 years ago

10.1016/j.str.2020.03.012

Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa
Cited by: 9
Author(s): Nathanael Caveney, Alexander J F Egan, Isabel Ayala, Cédric Laguri, C.S. Robb, Eefjan Breukink, Waldemar Vollmer, N.C.J. Strynadka, Jean-Pierre Simorre
Software Mentions: 1
Published: over 4 years ago

10.3390/toxins13040253

The Crystal Structure of Bacillus cereus HblL1
Cited by: 8
Author(s): Harley L. Worthy, Lainey J. Williamson, Husam Sabah Auhim, Stephen H. Leppla, Inka Sastalla, D. Dafydd Jones, P.J. Rizkallah, Colin Berry
Software Mentions: 1
Published: over 3 years ago

10.1186/s13063-017-1891-x

Head-to-head comparison of aggressive conventional therapy and three biological treatments and comparison of two de-escalation strategies in patients who respond to treatment: study protocol for a multicenter, randomized, open-label, blinded-assessor, phase 4 study
Cited by: 18
Author(s): Daniel Glinatsi, Marte Schrumpf Heiberg, Anna Rudin, Dan Nordström, Espen A. Haavardsholm, Björn Guðbjörnsson, Mikkel Østergaard, Till Uhlig, Gerður Gröndal, Kim Hørslev‐Petersen, Ronald F. van Vollenhoven, Merete Lund Hetland
Software Mentions: 1
Published: over 7 years ago

10.1107/S2052252516008113

Residue contacts predicted by evolutionary covariance extend the application of<i>ab initio</i>molecular replacement to larger and more challenging protein folds
Cited by: 16
Author(s): Felix Šimkovic, Jens M. H. Thomas, Ronan Keegan, Martyn Winn, Olga Mayans, Daniel J. Rigden
Software Mentions: 1
Published: over 8 years ago

10.1107/S2052252517005115

Applications of contact predictions to structural biology
Cited by: 36
Author(s): Felix Šimkovic, С. Г. Овчинников, David Baker, Daniel J. Rigden
Software Mentions: 1
Published: over 7 years ago