Ecosyste.ms: Papers

10.1371/journal.pone.0238665

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Cited by: 19
Author(s): Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Margarita Zachariou, George M. Spyrou
Software Mentions: 18
Published: over 3 years ago

10.3390/biom11020338

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations
Cited by: 1
Author(s): Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frąc, Jacek Panek, Boris Fumanal, Aurélie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stéphane Venisse
Software Mentions: 12
Published: about 3 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: over 5 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: almost 4 years ago

10.1099/mgen.0.000165

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection
Cited by: 45
Author(s): Jane Hawkey, David B. Ascher, Louise M. Judd, Ryan R. Wick, Xenia Kostoulias, Heather Cleland, Denis Spelman, Alex Padiglione, Anton Y. Peleg, Kathryn E. Holt
Software Mentions: 11
Published: about 6 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: over 3 years ago

10.1016/j.celrep.2020.107885

CD4+ T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features
Cited by: 9
Author(s): Alexander Greenshields‐Watson, Meriem Attaf, Bruce J. MacLachlan, Thomas Whalley, Cristina Rius, Aaron Wall, Alun G. Lloyd, Hywel Hughes, Kathryn E. Strange, Georgina H Mason, Andrea J. A. Schauenburg, Sarah Hulin-Curtis, James Geary, Yuan Chen, Sarah N. Lauder, Kathryn Smart, Dhanasekaran Vijaykrishna, Miguel L. Grau, Mikhail Shugay, Robert Andrews, Garry Dolton, P.J. Rizkallah, Awen Gallimore, Andrew K. Sewell, Andrew Godkin, David K. Cole
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pcbi.1009380

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Cited by: 11
Author(s): Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce
Software Mentions: 10
Published: over 2 years ago

10.7554/eLife.53278

GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm
Cited by: 25
Author(s): Arun Sharma, Lauren Wasson, Jon A. L. Willcox, Sarah U. Morton, Joshua M. Gorham, Daniel M. DeLaughter, Meraj Neyazi, Manuel Schmid, Radhika Agarwal, Min Young Jang, Christopher N. Toepfer, Tarsha Ward, Yuri Kim, Alexandre C. Pereira, Steven R. DePalma, Angela Tai, Seongwon Kim, David A. Conner, Daniel Bernstein, Bruce D. Gelb, Wendy K. Chung, Elizabeth Goldmuntz, George A. Porter, Martin Tristani‐Firouzi, Deepak Srivastava, Jonathan G. Seidman, Christine E. Seidman
Software Mentions: 9
Published: over 3 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-016-1321-1

GEN3VA: aggregation and analysis of gene expression signatures from related studies
Cited by: 17
Author(s): Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter M.U. Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma’ayan
Software Mentions: 9
Published: over 7 years ago

10.1016/j.molcel.2018.11.006

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains
Cited by: 117
Author(s): Jean-Philippe Lambert, S. Picaud, Takao Fujisawa, Huayun Hou, P. Savitsky, Liis Uusküla-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen‐Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St‐Denis, Joseph A. Newman, Manuel Stucki, Laurence Pelletier, Nuno Bandeira, Michael D. Wilson, P. Filippakopoulos, Anne‐Claude Gingras
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.203040

Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension
Cited by: 16
Author(s): Haoru Dong, Xiuchun Li, Mengsi Cai, Chi Zhang, Mao Wei-qi, Ying Wang, Qinying Xu, Mayun Chen, Liangxing Wang, Xiaoying Huang
Software Mentions: 9
Published: almost 3 years ago

10.3390/ijms22116160

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis
Cited by: 10
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Kheloud El Eshraky, Michał Górka, Bo-Eng Cheong, Erika Vanessa Jiménez-Posada, Dirk Walther, Aleksandra Skirycz, Ute Roessner, Joachim Kopka, Alexandre Augusto Pereira Firmino
Software Mentions: 9
Published: almost 3 years ago

10.3389/fphar.2021.621359

Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: about 3 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0023947

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction
Cited by: 19
Author(s): Christopher S. Poultney, Glenn L. Butterfoss, Michelle Gutwein, Kevin Drew, David Gresham, Kristin C. Gunsalus, Dennis Shasha, Richard Bonneau
Software Mentions: 8
Published: over 12 years ago

10.3390/molecules24213987

Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency
Cited by: 19
Author(s): Taremekedzwa Allan Sanyanga, Bilal Nizami, Özlem Tastan Bishop
Software Mentions: 8
Published: over 4 years ago

10.1186/s12906-020-02939-y

A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies
Cited by: 3
Author(s): Mengwei Ni, Xinkui Liu, Ziqi Meng, Shuyu Liu, Shanshan Jia, Yingying Liu, Wei Zhou, Jiarui Wu, Jingyuan Zhang, Siyu Guo, Jialin Li, Haojia Wang, Xiaomeng Zhang
Software Mentions: 8
Published: almost 4 years ago

10.1107/S2059798319011471

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in <i>Phenix</i>
Cited by: 3,483
Author(s): Dorothée Liebschner, Pavel V. Afonine, Matthew L. Baker, G. Bunkóczi, V.B. Chen, Tristan I. Croll, Bradley J. Hintze, Li Wei Hung, Swati Jain, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Billy K. Poon, Michael G. Prisant, R.J. Read, Jane S. Richardson, David C. Richardson, Massimo Sammito, Oleg Sobolev, Duncan H. Stockwell, Thomas C. Terwilliger, Alexandre Urzhumtsev, Lizbeth L. Videau, Christopher J. Williams, Paul D. Adams
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.36495

Firefly genomes illuminate parallel origins of bioluminescence in beetles
Cited by: 95
Author(s): Timothy R. Fallon, Sarah E. Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J. Martin, Adam J. Bewick, Megan G Behringer, Humberto Julio Debat, Isaac Wong, John C. Day, Anton Suvorov, Christian J. Silva, Kathrin F. Stanger‐Hall, David W. Hall, Robert J. Schmitz, David R. Nelson, Sara M. Lewis, Shuji Shigenobu, Seth Bybee, Amanda M. Larracuente, Yuichi Oba, Jing‐Ke Weng
Software Mentions: 8
Published: over 5 years ago

10.1016/j.molcel.2021.03.041

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network
Cited by: 28
Author(s): Colin M. Hammond, Hongyu Bao, Ivo A. Hendriks, Massimo Carraro, Alberto García-Nieto, Yanhong Liu, Nazaret Reverón-Gómez, Christos Spanos, Liu Chen, Juri Rappsilber, Michael L. Nielsen, Dinshaw J. Patel, Hongda Huang, Anja Groth
Software Mentions: 8
Published: almost 3 years ago

10.1107/S2053273319011446

Bayesian machine learning improves single-wavelength anomalous diffraction phasing
Cited by: 10
Author(s): María-José García-Bonete, Gergely Katona
Software Mentions: 7
Published: over 4 years ago

10.1186/s13321-019-0351-x

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data
Cited by: 25
Author(s): Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer
Software Mentions: 7
Published: about 5 years ago

10.1107/S2059798317007859

Recent developments in the<i>CCP-EM</i>software suite
Cited by: 266
Author(s): Tom Burnley, Colin M. Palmer, Martyn Winn
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12859-019-3099-4

DIRECT: RNA contact predictions by integrating structural patterns
Cited by: 14
Author(s): Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao, Chen Zeng
Software Mentions: 7
Published: over 4 years ago

10.1107/S0907444913007051

<i>OpenStructure</i>: an integrated software framework for computational structural biology
Cited by: 82
Author(s): Marco Biasini, Tobias Schmidt, Stefan Bienert, Valerio Mariani, Gabriel Studer, Juergen Haas, Niklaus Johner, Andreas Schenk, Ansgar Philippsen, Torsten Schwede
Software Mentions: 7
Published: about 11 years ago

10.7554/eLife.45403

The dynamic conformational landscape of the protein methyltransferase SETD8
Cited by: 37
Author(s): Shi Chen, Rafal Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fábio Pittella Silva, Kyle A. Beauchamp, W. Tempel, Hualiang Jiang, Kaixian Chen, R.J. Skene, Y. George Zheng, Peter J. Brown, Jian Jin, Cheng Luo, John D. Chodera, Minkui Luo
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0256990

Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
Cited by: 11
Author(s): Joe G Greener, David T. Jones
Software Mentions: 7
Published: over 2 years ago

10.3389/fonc.2021.681946

Prognostic Biomarkers on a Competitive Endogenous RNA Network Reveals Overall Survival in Triple-Negative Breast Cancer
Cited by: 3
Author(s): Wenxing Qin, Qi Feng, Jia Li, Ping Li, Yuan‐Sheng Zang
Software Mentions: 7
Published: almost 3 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12935-021-02212-3

Midkine promotes glioblastoma progression via PI3K-Akt signaling
Cited by: 14
Author(s): Beiquan Hu, Chao Qin, Li Li, Lei Wei, Xianlun Mo, Huasheng Fan, Yuanhua Lei, Feng Wang, Donghua Zou
Software Mentions: 7
Published: over 2 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: almost 4 years ago

10.1155/2021/8897313

Systematic Investigation of the Effect of Powerful Tianma Eucommia Capsule on Ischemic Stroke Using Network Pharmacology
Cited by: 4
Author(s): Pengcheng Feng, Guixia Li, Yuandong Huang, Jinhong Pei
Software Mentions: 7
Published: almost 3 years ago

10.1093/gigascience/giaa059

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats
Cited by: 16
Author(s): Yocelyn T. Gutiérrez-Guerrero, Enrique Ibarra-Laclette, Carlos Martı́nez del Rio, Josué Barrera‐Redondo, Eria A. Rebollar, Jorge Ortega, Livia León‐Paniagua, Araxi O. Urrutia, Erika Aguirre‐Planter, Luis E. Eguiarte
Software Mentions: 6
Published: almost 4 years ago

10.1093/genetics/iyab014

Split-wrmScarlet and split-sfGFP: tools for faster, easier fluorescent labeling of endogenous proteins in <i>Caenorhabditis elegans</i>
Cited by: 13
Author(s): Jérôme Goudeau, Catherine S. Sharp, Jonathan S. Paw, Laura Savy, Manuel D. Leonetti, Andrew G. York, Dustin L. Updike, Cynthia Kenyon, Maria Ingaramo
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-23913-2

Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak
Cited by: 3
Author(s): Sophie Andrews, Yonghong Zhang, Tao Dong, Sarah Rowland‐Jones, Sunetra Gupta, Joakim Esbjörnsson
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pcbi.1008807

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
Cited by: 7
Author(s): Andreas Haahr Larsen, Lilya Tata, Laura John, Mark S. P. Sansom
Software Mentions: 6
Published: over 2 years ago

10.1186/s13321-016-0180-0

Mapping the 3D structures of small molecule binding sites
Cited by: 13
Author(s): Joshua Meyers, Nathan Brown, Julian Blagg
Software Mentions: 6
Published: over 7 years ago

10.1128/JVI.00500-19

Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity
Cited by: 81
Author(s): Alan D. Russell, Elizaveta Elshina, Jacob R. Kowalsky, Aartjan J.W. te Velthuis, Jesse D. Bloom
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2019.00618

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: about 5 years ago

10.3390/molecules26185574

Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma
Cited by: 2
Author(s): Filipe G A Estrada, Silvia Miccoli, Natália Aniceto, Alfonso T. García-Sosa, Rita C. Guedes
Software Mentions: 6
Published: over 2 years ago

10.1371/journal.pone.0052884

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
Cited by: 17
Author(s): Mark L. Grimes, Wan-Jui Lee, Laurens van der Maaten, Paul Shannon
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pgen.1009645

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: almost 3 years ago

10.1107/S0907444909052925

<i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solution
Cited by: 19,578
Author(s): Paul D. Adams, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Ian Davis, Nathaniel Echols, Jeffrey J. Headd, Li Wei Hung, Gary J. Kapral, Ralf W. Grosse‐Kunstleve, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Peter H. Zwart
Software Mentions: 6
Published: over 14 years ago

10.7717/peerj.4013

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Cited by: 26
Author(s): Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern, Pierre Poulain
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.60265

The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism
Cited by: 20
Author(s): Jessica J. Stanisich, Dawid Zyla, Pavel Afanasyev, Jianlin Xu, Anne Kipp, Eric Olinger, Olivier Devuyst, Martin Pilhofer, Daniel Boehringer, Rudi Glockshuber
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.66797

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
Cited by: 6
Author(s): Kai He, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-ichiro Kawada, Mark S. Springer, Michael Berenbrink, Kevin L. Campbell
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.66398

Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ
Cited by: 7
Author(s): Yang Zhang, Gerd Bobe, Cristobal L. Miranda, Malcolm B. Lowry, Victor L. Hsu, Christiane V. Löhr, Carmen P. Wong, Donald Β. Jump, Matthew M. Robinson, Thomas J. Sharpton, Claudia S. Maier, Jan F. Stevens, Adrian F. Gombart
Software Mentions: 6
Published: almost 3 years ago

10.1093/molbev/msab172

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages
Cited by: 12
Author(s): Antonello Di Nardo, Luca Ferretti, Jemma Wadsworth, Valérie Mioulet, Boris Gelman, Sharon Karniely, A. V. Scherbakov, Ghulam Ziay, Fuat Özyörük, Ünal Parlak, Pelin Tuncer‐Göktuna, Reza Hassanzadeh, Mehdi Khalaj, Seyed Mohsen Dastoor, Darab Abdollahi, Ehtisham-ul-Haq Khan, Muhammad Afzal, Manzoor Hussain, Nick J. Knowles, Donald P. King
Software Mentions: 6
Published: almost 3 years ago

10.1186/s13321-020-0415-y

The C++ programming language in cheminformatics and computational chemistry
Cited by: 13
Author(s): Dmitrii N. Rassokhin
Software Mentions: 6
Published: over 4 years ago

10.1016/j.str.2015.12.011

The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope
Cited by: 79
Author(s): Tyler Reddy, Mark S. P. Sansom
Software Mentions: 6
Published: about 8 years ago

10.1111/mpp.13003

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode <i>Hirschmanniella oryzae</i> , increase host susceptibility by manipulating secondary metabolite content of rice
Cited by: 8
Author(s): Lander Bauters, Tina Kyndt, Tim De Meyer, Kris Morreel, Wout Boerjan, Hannes Lefevere, Godelieve Gheysen
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.51179

Structure of a mitochondrial ATP synthase with bound native cardiolipin
Cited by: 65
Author(s): A. Muhleip, Sarah McComas, Alexey Amunts
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0063906

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
Cited by: 311
Author(s): Sergey Lyskov, Fang Chieh Chou, Shane Ó Conchúir, Bryan S. Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D. Weitzner, P. Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J. Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J. Gray, Rhiju Das
Software Mentions: 5
Published: almost 11 years ago

10.1186/1743-422X-8-318

Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein
Cited by: 5
Author(s): Beata Hasiów‐Jaroszewska, Anna Czerwoniec, H. Pospieszny, Santiago F. Elena
Software Mentions: 5
Published: almost 13 years ago

10.1371/journal.ppat.1009729

Definition of the immune evasion-replication interface of rabies virus P protein
Cited by: 10
Author(s): Jingyu Zhan, Angela R. Harrison, Stephanie Portelli, Thanh Bình Nguyễn, Isshu Kojima, Siqiong Zheng, Fei Yan, Tsutomu Matsui, Stephen M. Rawlinson, Ashish Sethi, Naoto Ito, David B. Ascher, Gregory W. Moseley, Paul R. Gooley
Software Mentions: 5
Published: almost 3 years ago

10.7554/eLife.38795

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin
Cited by: 20
Author(s): Angela M Phillips, Michael B. Doud, Luna O Gonzalez, Vincent Butty, Yu‐Shan Lin, Jesse D. Bloom, Matthew D. Shoulders
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0256691

Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network
Cited by: 1
Author(s): Julian Nazet, Elmar Lang, Rainer Merkl
Software Mentions: 5
Published: over 2 years ago

10.12688/f1000research.17456.1

pdb-tools: a swiss army knife for molecular structures
Cited by: 81
Author(s): João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0066856

The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite
Cited by: 23
Author(s): Jared Adolf-Bryfogle, Roland L. Dunbrack
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0100736

Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions
Cited by: 125
Author(s): Jasmin F. Sydow, Florian Lipsmeier, Vincent Larraillet, Maximiliane Hilger, Bjoern Mautz, Michael Mølhøj, Jan Kuentzer, Stefan Klostermann, Juergen Schoch, Hans R. Voelger, Jörg T. Regula, Patrick Cramer, Apollon Papadimitriou, Hubert Kettenberger
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pbio.3000557

BMPR2 acts as a gatekeeper to protect endothelial cells from increased TGFβ responses and altered cell mechanics
Cited by: 65
Author(s): Christian Hiepen, Jerome Jatzlau, Susanne Hildebrandt, Branka Kampfrath, Melis Göktas, Arunima Murgai, José Luis Cuellar Camacho, Rainer Haag, Clemens Ruppert, Gerhard Sengle, Elisabetta Ada Cavalcanti‐Adam, Kerstin Blank, Petra Knaus
Software Mentions: 5
Published: over 4 years ago

10.1107/S2052252518000519

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
Cited by: 23
Author(s): Michael E. Wall
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.58660

Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms
Cited by: 37
Author(s): Katherine E. Huffer, Antoniya A. Aleksandrova, Andrés Jara-Oseguera, Lucy R. Forrest, Kenton J. Swartz
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-39276-1

Insights into the antigenic advancement of influenza A(H3N2) viruses, 2011–2018
Cited by: 45
Author(s): Patricia A. Jorquera, Vasiliy P. Mishin, Anton Chesnokov, Ha Nguyen, Brian R. Mann, Rebecca Garten, John Barnes, Erin Hodges, Juan de la Cruz, Xinhua Xu, Jackie Katz, David E. Wentworth, Larisa V. Gubareva
Software Mentions: 5
Published: about 5 years ago

10.1093/bib/bbaa150

Recent advances in user-friendly computational tools to engineer protein function
Cited by: 30
Author(s): Carlos Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0198632

Allosteric binding sites in Rab11 for potential drug candidates
Cited by: 9
Author(s): Ammu Prasanna Kumar, Suryani Lukman
Software Mentions: 5
Published: almost 6 years ago

10.1002/mgg3.1106

Structural analysis of pathogenic missense mutations in <i>GABRA2</i> and identification of a novel de novo variant in the desensitization gate
Cited by: 7
Author(s): Alba Sanchis‐Juan, Marcia Anahí Hasenahuer, James Alexander Baker, Amy McTague, Katy Barwick, Manju A. Kurian, Sofia Duarte, Nihr BioResource, Keren Carss, Janet M. Thornton, F. Lucy Raymond
Software Mentions: 5
Published: about 4 years ago

10.15252/embj.2020106807

Cryo‐EM structure of native human uromodulin, a zona pellucida module polymer
Cited by: 24
Author(s): A. Stsiapanava, Chenrui Xu, Martina Brunati, Sara Zamora-Caballero, Céline Schaeffer, Marcel Bokhove, Ling Han, Hans Hebert, Marta Carroni, Shigeki Yasumasu, Luca Rampoldi, Bin Wu, Luca Jovine
Software Mentions: 5
Published: over 3 years ago

10.1107/S0021889812017293

Graphical tools for macromolecular crystallography in<i>PHENIX</i>
Cited by: 136
Author(s): Nathaniel Echols, Ralf W. Grosse‐Kunstleve, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Jeffrey J. Headd, Airlie J. McCoy, Nigel W. Moriarty, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Paul D. Adams
Software Mentions: 5
Published: almost 12 years ago

10.3390/plants10061092

Polymorphism in the Chloroplast ATP Synthase Beta-Subunit Is Associated with a Maternally Inherited Enhanced Cold Recovery in Cucumber
Cited by: 5
Author(s): Madeline W. Oravec, Michael J. Havey
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12936-020-03512-1

Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study
Cited by: 5
Author(s): Rita Afriyie Boateng, Özlem Tastan Bishop, Thommas M. Musyoka
Software Mentions: 5
Published: over 3 years ago

10.3390/plants9030323

Secondary Structure of Chloroplast mRNAs In Vivo and In Vitro
Cited by: 8
Author(s): Piotr Gawroński, Aleksandra Pałac, Lars B. Scharff
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pbio.1001229

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Cited by: 91
Author(s): Robert K. Bradley, Jason J. Merkin, Nicole Lambert, Christopher B. Burge
Software Mentions: 5
Published: over 12 years ago

10.7554/eLife.67518

The structure of photosystem I from a high-light-tolerant cyanobacteria
Cited by: 13
Author(s): Zachary Dobson, Safa Ahad, Jackson Vanlandingham, Hila Toporik, Natalie Vaughn, Michael Vaughn, Dewight Williams, Michael Reppert, Petra Fromme, Yuval Mazor
Software Mentions: 5
Published: over 2 years ago

10.1128/AEM.03074-15

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an <i>In Vivo</i> Competition Assay
Cited by: 13
Author(s): Zhao Jin, Sara C. Di Rienzi, Anders Janzon, Jeff J. Werner, Largus T. Angenent, Jeffrey L. Dangl, Douglas M. Fowler, Ruth E. Ley
Software Mentions: 5
Published: about 8 years ago

10.1155/2019/6151587

Direct Extracellular Electron Transfer of the <i>Geobacter sulfurreducens</i> Pili Relevant to Interaromatic Distances
Cited by: 6
Author(s): Chuanjun Shu, Qunzhi Zhu, Ke Xiao, Yanbing Hou, Haibo Ma, Jing Ma, Xiao Sun
Software Mentions: 5
Published: over 4 years ago

10.1242/bio.040683

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Cited by: 4
Author(s): Isabel Reuter, Jana Jäckels, Susanne Kneitz, Jochen Kuper, Klaus–Peter Lesch, Christina Lillesaar
Software Mentions: 5
Published: over 5 years ago

10.1128/mBio.03202-19

Reducing Aspergillus fumigatus Virulence through Targeted Dysregulation of the Conidiation Pathway
Cited by: 18
Author(s): James I P Stewart, Vinicius M. Fava, Joshua D. Kerkaert, Adithya S. Subramanian, Fabrice N. Gravelat, Mélanie Lehoux, P. Lynne Howell, Robert A. Cramer, Donald C. Sheppard
Software Mentions: 5
Published: about 4 years ago

10.3389/fphys.2021.652799

Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential
Cited by: 45
Author(s): Kruthi Suvarna, Deeptarup Biswas, Medha Gayathri J Pai, Arup Acharjee, Renuka Bankar, Viswanthram Palanivel, Akanksha Salkar, Ayushi Verma, Amrita Mukherjee, Manisha Choudhury, Saicharan Ghantasala, Susmita Ghosh, Avinash Singh, Arghya Banerjee, Apoorva Badaya, Surbhi Bihani, Gaurish Loya, Krishi Mantri, Ananya Burli, Jyotirmoy Roy, Alisha Srivastava, Sachee Agrawal, Om Shrivastav, Jayanthi Shastri, Sanjeeva Srivastava
Software Mentions: 5
Published: about 3 years ago

10.3389/fpls.2020.00948

Systematic Review of Plant Ribosome Heterogeneity and Specialization
Cited by: 49
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Joachim Kopka
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0109715

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome
Cited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0240932

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1
Cited by: 27
Author(s): Guillaume Gaullier, Genevieve Roberts, Uma M. Muthurajan, Samuel Bowerman, Johannes Rudolph, Jyothi Mahadevan, Asmita Jha, Purushka S. Rae, Karolin Luger
Software Mentions: 5
Published: over 3 years ago

10.1186/s12862-016-0743-8

Adaptive patterns in the p53 protein sequence of the hypoxia- and cancer-tolerant blind mole rat Spalax
Cited by: 8
Author(s): Vered Domankevich, Yarden Opatowsky, Assaf Malik, Abraham B. Korol, Zeev Frenkel, Irena Manov, Aaron Avivi, Imad Shams
Software Mentions: 5
Published: over 7 years ago

10.1186/s12915-021-01139-5

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching
Cited by: 21
Author(s): Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Olga Douvropoulou, Qingtian Guan, Francisco J. Guzmán‐Vega, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Júnior, Júlio César de Souza, Sílvia Bahadian Moreira, Zelinda Maria Braga Hirano, Alcides Pissinatti, Maria de Fátima Ferreira-da-Cruz, Ricardo Lourenço de Oliveira, Stefan T. Arold, Daniel C. Jeffares, Patrícia Brasil, Cristiana Ferreira Alves de Brito, Richard Culleton, Cláudio Tadeu Daniel-Ribeiro, Arnab Pain
Software Mentions: 5
Published: over 2 years ago

10.1371/journal.pcbi.1004867

An Introduction to Programming for Bioscientists: A Python-Based Primer
Cited by: 46
Author(s): Berk Ekmekci, Charles E. McAnany, Cameron Mura
Software Mentions: 5
Published: almost 8 years ago

10.1107/S0907444911007281

Presenting your structures: the<i>CCP</i>4<i>mg</i>molecular-graphics software
Cited by: 1,079
Author(s): Stuart McNicholas, E. A. Potterton, K.S. Wilson, M.E.M. Noble
Software Mentions: 5
Published: about 13 years ago

10.1371/journal.pone.0252759

Antimicrobial activity of methanolic extracts of Vernonia cinerea against Xanthomonas oryzae and identification of their compounds using in silico techniques
Cited by: 6
Author(s): Tushar Joshi, Satish Chandra Pandey, Priyanka Maiti, Manish Kumar Tripathi, Ashutosh Paliwal, Mahesha Nand, Priyanka Sharma, Mukesh Samant, Veena Pande, Subhash Chandra
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12859-019-2645-4

reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction
Cited by: 5
Author(s): Risa Karakida Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1008988

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Cited by: 10
Author(s): Nikolina Šoštarić, Vera van Noort
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12862-018-1297-8

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs
Cited by: 15
Author(s): Ben Auxier, Jaclyn Dee, Mary L. Berbee, Michelle Momany
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.05421

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
Cited by: 106
Author(s): Monarin Uervirojnangkoorn, Oliver B. Zeldin, A.Y. Lyubimov, Johan Hattne, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, William I. Weis
Software Mentions: 5
Published: about 9 years ago

10.7554/eLife.02978

The pseudo GTPase CENP-M drives human kinetochore assembly
Cited by: 107
Author(s): Federica Basilico, Stefano Maffini, John R. Weir, Daniel Prumbaum, Ana M. Rojas, Tomasz Zimniak, De Antoni A, Sadasivam Jeganathan, Beate Voss, Suzan van Gerwen, Veronica Krenn, Lucia Massimiliano, Alfonso Valencia, Ingrid R. Vetter, Franz Herzog, Stefan Raunser, Sebastiano Pasqualato, Andrea Musacchio
Software Mentions: 5
Published: almost 10 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: over 10 years ago

10.7554/eLife.46070

Large protein organelles form a new iron sequestration system with high storage capacity
Cited by: 83
Author(s): Tobias W. Giessen, Benjamin J. Orlando, Andrew A Verdegaal, Melissa G. Chambers, Jules Gardener, David C. Bell, Gabriel Birrane, Maofu Liao, Pamela A. Silver
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.55132

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties
Cited by: 26
Author(s): Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, Gregory R. Bowman
Software Mentions: 5
Published: almost 4 years ago

10.1107/S1399004715007415

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles
Cited by: 14
Author(s): A.H. Van Benschoten, Pavel V. Afonine, Thomas C. Terwilliger, Michael E. Wall, Colin J. Jackson, Nicholas K. Sauter, Paul D. Adams, Alexandre Urzhumtsev, James S. Fraser
Software Mentions: 5
Published: almost 9 years ago

10.1107/S1399004715009220

From bacterial to human dihydrouridine synthase: automated structure determination
Cited by: 12
Author(s): Fiona Whelan, Huw T. Jenkins, Samuel C. Griffiths, Robert T. Byrne, E.J. Dodson, A.A. Antson
Software Mentions: 5
Published: almost 9 years ago

10.1107/S2059798317000031

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode
Cited by: 18
Author(s): Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, Cameron Mura
Software Mentions: 5
Published: about 7 years ago