cran: RAPTOR | Projects | Ecosyste.ms: Papers

10.1186/1472-6807-9-28

Improving consensus contact prediction via server correlation reduction
Cited by: 27
Author(s): Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li
Software Mentions: 4
Published: over 15 years ago

Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes
Cited by: 9
Author(s): Bénédicte Gnangnon, Aline Fréville, Kátia Cailliau, Catherine Leroy, Caroline De Witte, David Tulasne, Alain Martoriarti, Vincent Jung, Ida Chiara Guerrera, Sabrina Marion, Jamal Khalife, Christine Pierrot
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.01757-19

Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output
Cited by: 10
Author(s): Lindsey O’Neal, Jessica M. Gullett, Anastasia Aksenova, Adam Keith Hubler, Ariane Briegel, Davi R. Ortega, Andreas Kjær, Grant J. Jensen, Gladys Alexandre
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0050200

eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures
Cited by: 32
Author(s): Michał Bryliński, Daswanth Lingam
Software Mentions: 3
Published: about 12 years ago

10.3389/fpls.2021.702442

Wood Anatomy of Douglas-Fir in Eastern Arizona and Its Relationship With Pacific Basin Climate
Cited by: 6
Author(s): Daniel Balanzategui, Henry Nordhauß, Ingo Heinrich, Franco Biondi, Nicholas Miley, Alexander Hurley, Emanuele Ziaco
Software Mentions: 3
Published: over 3 years ago

10.1016/j.csbj.2017.01.008

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase
Cited by: 14
Author(s): Katja Venko, Amrita Roy Choudhury, Marjana Novič
Software Mentions: 3
Published: almost 8 years ago

10.1042/BCJ20200715

Current data processing strategies for cryo-electron tomography and subtomogram averaging
Cited by: 35
Author(s): Euan Pyle, Giulia Zanetti
Software Mentions: 3
Published: over 3 years ago

10.1186/s13643-019-1070-0

Introducing RAPTOR: RevMan Parsing Tool for Reviewers
Cited by: 32
Author(s): Lena Schmidt, Farhad Shokraneh, Kirsten Steinhausen, Clive E Adams
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.32471

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis
Cited by: 157
Author(s): Saman Hussain, Carl N. Wivagg, Piotr Szwedziak, Felix Wong, Kaitlin Schaefer, Thierry Izoré, Lars D. Renner, Matthew J Holmes, Yingjie Sun, Alexandre W. Bisson‐Filho, Suzanne Walker, Ariel Amir, Jan Löwe, Ethan C. Garner
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.04601

Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division
Cited by: 200
Author(s): Piotr Szwedziak, Qing Wang, Tanmay A. M. Bharat, M. Tsim, Jan Löwe
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-10-366

(PS)2-v2: template-based protein structure prediction server
Cited by: 97
Author(s): Chih-Chieh Chen, Jenn Kang Hwang, Jinn-Moon Yang
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0017215

Incorporation of Local Structural Preference Potential Improves Fold Recognition
Cited by: 15
Author(s): Yun Hu, Xiaoxi Dong, Aiping Wu, Yang Cao, Liqing Tian, Taijiao Jiang
Software Mentions: 2
Published: almost 14 years ago

10.1002/jcsm.12496

Skeletal muscle mTORC1 regulates neuromuscular junction stability
Cited by: 38
Author(s): Martina Baraldo, Alessia Geremia, Marco Pirazzini, Leonardo Nogara, Francesca Solagna, Clara Türk, Hendrik Nolte, Vanina Romanello, Aram Megighian, Simona Boncompagni, Marcus Krüger, Marco Sandri, Bert Blaauw
Software Mentions: 2
Published: about 5 years ago

10.1093/jxb/eraa595

Isometric scaling to model water transport in conifer tree rings across time and environments
Cited by: 8
Author(s): Irina V. Sviderskaya, Е. А. Ваганов, Marina V. Fonti, Patrick Fonti
Software Mentions: 2
Published: about 4 years ago

10.3390/ma12101653

Enhanced Sensing and Data Processing System for Continuous Profiling of Pavement Deflection
Cited by: 2
Author(s): Boo Hyun Nam, Kenneth H. Stokoe, Heejung Youn
Software Mentions: 2
Published: over 5 years ago

10.1186/s13017-021-00390-z

Systematic review of the efficacy of a hybrid operating theatre in the management of severe trauma
Cited by: 2
Author(s): Chun Yuet Khoo, Yi Song Terence Liew, Sachin Mathur
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-15-S11-S14

Improving protein fold recognition by random forest
Cited by: 51
Author(s): Taeho Jo, Jianlin Cheng
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pbio.3000165

γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures
Cited by: 69
Author(s): Josie L. Ferreira, Forson Gao, Florian Roßmann, Andrea Nans, Susanne Brenzinger, Rohola Hosseini, Amanda J. Wilson, Ariane Briegel, Kai M. Thormann, Peter B. Rosenthal, Morgan Beeby
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2012-13-8-r76

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
Cited by: 44
Author(s): Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger
Software Mentions: 1
Published: almost 13 years ago

10.1186/1754-1611-1-3

Development of a Cryptosporidium oocyst assay using an automated fiber optic-based biosensor
Cited by: 17
Author(s): Marianne F. Kramer, Graham Vesey, Natasha L Look, Ben R. Herbert, Joyce M. Simpson-Stroot, Daniel V. Lim
Software Mentions: 1
Published: about 17 years ago

10.1186/s13049-016-0196-5

Preperitoneal pelvic packing in patients with hemodynamic instability due to severe pelvic fracture: early experience in a Korean trauma center
Cited by: 49
Author(s): Ji Young Jang, Hongjin Shim, Pil Young Jung, Seongyup Kim, Keum Seok Bae
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep17573

Improving Protein Fold Recognition by Deep Learning Networks
Cited by: 110
Author(s): Taeho Jo, Jie Hou, Jesse Eickholt, Jianlin Cheng
Software Mentions: 1
Published: about 9 years ago

10.1038/srep19915

Predictability of the dispersion of Fukushima-derived radionuclides and their homogenization in the atmosphere
Cited by: 23
Author(s): Róbert Mészáros, Ádám Leelőssy, Tibor Kovács, István Lagzi
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-18115-1

Evolution of higher torque in Campylobacter-type bacterial flagellar motors
Cited by: 61
Author(s): Bonnie Chaban, Izaak Coleman, Morgan Beeby
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-021-94132-5

VHL suppresses RAPTOR and inhibits mTORC1 signaling in clear cell renal cell carcinoma
Cited by: 10
Author(s): Athina Ganner, Christina Gehrke, Marinella Klein, Lena Thegtmeier, Tanja Matulenski, Laura Wingendorf, Lu Wang, Felicitas Pilz, Lars Greidl, Lisa Meid, Fruzsina Kotsis, Gerd Walz, Ian J. Frew, Elke Neumann-Haefelin
Software Mentions: 1
Published: over 3 years ago

10.3390/s141222313

Evaluation of Optical Detection Platforms for Multiplexed Detection of Proteins and the Need for Point-of-Care Biosensors for Clinical Use
Cited by: 63
Author(s): Samantha Spindel, Kim E. Sapsford
Software Mentions: 1
Published: about 10 years ago

10.1128/mBio.02286-19

Diversification of Campylobacter jejuni Flagellar C-Ring Composition Impacts Its Structure and Function in Motility, Flagellar Assembly, and Cellular Processes
Cited by: 20
Author(s): Louie Henderson, Teige R. S. Matthews-Palmer, Connor J. Gulbronson, Deborah A. Ribardo, Morgan Beeby, David R. Hendrixson
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.73099

In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography
Cited by: 12
Author(s): Mohammed Kaplan, Georges Chreifi, Lauren Ann Metskas, Janine Liedtke, Cecily R. Wood, Catherine M. Oikonomou, William J Nicolas, Poorna Subramanian, Lori A. Zacharoff, Yuhang Wang, Yi-Wei Chang, Morgan Beeby, Megan J. Dobro, Yongtao Zhu, Mark J. McBride, Ariane Briegel, Carrie L. Shaffer, Grant J. Jensen
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.68799

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace
Cited by: 5
Author(s): Maren Heimhalt, Alex Berndt, Jane L. Wagstaff, Madhanagopal Anandapadamanaban, Olga Perišić, Sarah Maslen, Stephen H. McLaughlin, Chunxue Yu, Glenn R. Masson, Andreas Boland, Xiaodan Ni, Keitaro Yamashita, Garib N. Murshudov, Mark Skehel, Stefan Freund, Roger L. Williams
Software Mentions: 1
Published: over 3 years ago

10.1152/ajpendo.00237.2016

Benzimidazole derivative small-molecule 991 enhances AMPK activity and glucose uptake induced by AICAR or contraction in skeletal muscle
Cited by: 48
Author(s): Laurent Bultot, Thomas E. Jensen, Yu‐Chiang Lai, Agnete B. Madsen, Caterina Collodet, Samanta Kviklyte, Maria Deák, Arash Yavari, Marc Foretz, Sahar Ghaffari, Mohamed Bellahcene, Houman Ashrafian, Mark H. Rider, Erik A. Richter, Kei Sakamoto
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms22126237

The Molecular Characteristics of Non-Clear Cell Renal Cell Carcinoma: What’s the Story Morning Glory?
Cited by: 13
Author(s): Andrea Marchetti, Matteo Rosellini, Veronica Mollica, Alessandro Rizzo, Elisa Tassinari, Giacomo Nuvola, Alessia Cimadamore, Matteo Santoni, Michelangelo Fiorentino, Rodolfo Montironi, Francesco Massari
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-10-S1-S38

Prediction of RNA secondary structure with pseudoknots using integer programming
Cited by: 51
Author(s): Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-15-22

BioShell-Threading: versatile Monte Carlo package for protein 3D threading
Cited by: 18
Author(s): Paweł Gniewek, Andrzej Koliński, Andrzej Kloczkowski, Dominik Gront
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-12-S1-S54

Incorporating Ab Initio energy into threading approaches for protein structure prediction
Cited by: 6
Author(s): Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Wei-Mou Zheng, Dongbo Bu
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12885-020-07322-1

UBR-box containing protein, UBR5, is over-expressed in human lung adenocarcinoma and is a potential therapeutic target
Cited by: 7
Author(s): Kumar Saurabh, Parag P. Shah, Mark A. Doll, Leah J. Siskind, Levi J. Beverly
Software Mentions: 1
Published: over 4 years ago

10.1186/1472-6807-5-6

A comprehensive update of the sequence and structure classification of kinases
Cited by: 107
Author(s): Sara Cheek, Krzysztof Ginalski, Hong Zhang, Nick V. Grishin
Software Mentions: 1
Published: almost 20 years ago

10.3390/biom7040077

Evolutionary Conservation of the Components in the TOR Signaling Pathways
Cited by: 87
Author(s): Hisashi Tatebe, Kazuhiro Shiozaki
Software Mentions: 1
Published: about 7 years ago

10.1111/mmi.14525

In situ structure of the <i>Caulobacter crescentus</i> flagellar motor and visualization of binding of a CheY‐homolog
Cited by: 19
Author(s): Florian Roßmann, Isabelle Hug, Matteo Sangermani, Urs Jenal, Morgan Beeby
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.11570

Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from <i>Bacillus cereus</i> RSA1
Cited by: 9
Author(s): Chhavi Sharma, Arti Nigam, Rajni Singh
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.0040032

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders
Cited by: 254
Author(s): Angela M. Hancock, David B. Witonsky, Adam S. Gordon, Gidon Eshel, Jonathan K. Pritchard, Graham Coop, Anna Di Rienzo
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0180051

Carbohydrate-mediated responses during zygotic and early somatic embryogenesis in the endangered conifer, Araucaria angustifolia
Cited by: 26
Author(s): Bruno Viana Navarro, Paula Elbl, Amanda P. De Souza, Leandro Francisco de Oliveira, Amanda Ferreira Macedo, André Luis Wendt dos Santos, Marcos Silveira Buckeridge, Eny Iochevet Segal Floh
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0172312

Numerical simulations of atmospheric dispersion of iodine-131 by different models
Cited by: 12
Author(s): Ádám Leelőssy, Róbert Mészáros, Attila Kovács, István Lagzi, Tibor Kovács
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.csbj.2020.11.007

Homology modeling in the time of collective and artificial intelligence
Cited by: 51
Author(s): Tareq Hameduh, Yazan Haddad, Vojtěch Adam, Zbyněk Heger
Software Mentions: 1
Published: almost 5 years ago

10.1186/s41512-021-00093-8

Rapid community point-of-care testing for COVID-19 (RAPTOR-C19): protocol for a platform diagnostic study
Cited by: 5
Author(s): Brian D Nicholson, Gail Hayward, P Turner, Joseph Lee, Alexandra Deeks, Mary Logan, Aaron William Moore, Anna Seeley, Thomas R Fanshawe, Jason Oke, Constantinos Koshiaris, James P Sheppard, Uy Hoang, Vaishnavi Parimalanathan, George Edwards, Harshana Liyange, Julian Sherlock, Rachel Byford, Maria Zambon, Joanna Ellis, Jamie Lopez Bernal, Gayatri Amirthalingam, Ezra Linley, Ray Borrow, Gary Howsam, Sophie Baines, Filipa Ferreira, Simon de Lusignan, Rafael Perera, F D Richard Hobbs
Software Mentions: 1
Published: almost 4 years ago

10.3390/foods10020421

The Occurrence of Skeletons of Silicoflagellata and Other Siliceous Bioparticles in Floral Honeys
Cited by: 1
Author(s): Donát Magyar, Paulian Dumitrică, Anna Mura-Mészáros, Zsófia Medzihradszky, Ádám Leelőssy, Simona Saint Martin
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.612239

Analysis of Cell–Cell Bridges in Haloferax volcanii Using Electron Cryo-Tomography Reveal a Continuous Cytoplasm and S-Layer
Cited by: 12
Author(s): Shamphavi Sivabalasarma, Hanna Wetzel, Phillip Nußbaum, Chris van der Does, Morgan Beeby, Sonja‐Verena Albers
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2021.643180

The “Jack-of-all-Trades” Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium
Cited by: 4
Author(s): Josie L. Ferreira, Izaak Coleman, Max L. Addison, Tobias Zachs, Bonnie Chaban, Kristin Wuichet, Morgan Beeby
Software Mentions: 1
Published: over 3 years ago

10.3389/fpls.2020.00016

The Importance of TOR Kinase in Plant Development
Cited by: 39
Author(s): Kirsty McCready, Victoria Spencer, Min Soo Kim
Software Mentions: 1
Published: almost 5 years ago

Projects: cran: RAPTOR

Papers Mentioning RAPTOR 48