Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: rosetta

https://packages.ecosyste.ms/registries/pypi.org/packages/rosetta

Tools, wrappers, etc... for data science with a concentration on text processing
8 versions
Latest release: over 9 years ago
1 dependent package
1,716 downloads last month

Papers Mentioning rosetta 16

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: about 5 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: over 9 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: over 11 years ago

10.1186/s13072-020-00355-7

N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum
Cited by: 11
Author(s): Gayathri Govindaraju, Rajashekar Varma Kadumuri, Devadathan Valiyamangalath Sethumadhavan, C. A. Jabeena, Sreenivas Chavali, Arumugam Rajavelu
Software Mentions: 4
Published: about 4 years ago

10.3390/cells9081776

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore
Cited by: 22
Author(s): Mourdas Mohamed, Nguyet Thi-Minh Dang, Yuki Ogyama, Nelly Burlet, Bruno Mugat, Matthieu Boulesteix, Vincent Mérel, Philippe Veber, Judit Salces-Ortiz, Dany Séverac, Alain Pélisson, Cristina Vieira, François Sabot, Marie Fablet, Séverine Chambeyron
Software Mentions: 4
Published: over 4 years ago

10.1186/1472-6807-8-46

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
Cited by: 10
Author(s): Yoshihide Makino, Nobuhide Itoh
Software Mentions: 4
Published: almost 17 years ago

10.1371/journal.pcbi.1008061

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
Cited by: 16
Author(s): Brian Coventry, David Baker
Software Mentions: 4
Published: over 3 years ago

10.1007/s10969-012-9129-3

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
Cited by: 132
Author(s): Thomas C. Terwilliger, Frank DiMaio, R.J. Read, David Baker, G. Bunkóczi, Paul D. Adams, Ralf W. Grosse‐Kunstleve, Pavel V. Afonine, Nathaniel Echols
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0020161

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Cited by: 481
Author(s): Sarel J. Fleishman, Andrew Leaver‐Fay, Jacob E. Corn, Eva-Maria Strauch, Sagar D. Khare, Nobuyasu Koga, Justin Ashworth, Patricia Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, David Baker
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0240450

Assessing multiple score functions in Rosetta for drug discovery
Cited by: 18
Author(s): Shannon Toney Smith, Jens Meiler
Software Mentions: 3
Published: about 4 years ago

10.1038/srep26847

Protein rethreading: A novel approach to protein design
Cited by: 4
Author(s): Sayeh Agah, Sandra Poulos, A Kosinsky Yu, Iga Kucharska, Salem Faham
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.54639

Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering
Cited by: 29
Author(s): Friso S. Aalbers, Maximilian J. L. J. Fürst, S. Rovida, Miloš Trajković, J. Rubén Gómez Castellanos, Sebastian Bartsch, Andreas Vogel, Andrea Mattevi, Marco W. Fraaije
Software Mentions: 3
Published: over 4 years ago

10.1107/S0907444912015636

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement
Cited by: 35
Author(s): Thomas C. Terwilliger, Randy J. Read, Paul D. Adams, Axel T. Brunger, Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Li Wei Hung
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0019230

De Novo Enzyme Design Using Rosetta3
Cited by: 260
Author(s): Florian Richter, Andrew Leaver‐Fay, Sagar D. Khare, Sinisa Bjelic, David C. Baker
Software Mentions: 2
Published: over 13 years ago

10.1107/S0907444913017770

Model morphing and sequence assignment after molecular replacement
Cited by: 33
Author(s): Thomas C. Terwilliger, Randy J. Read, Paul D. Adams, Axel T. Brunger, Pavel V. Afonine, Li Wei Hung
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-019-57279-w

Affinity-matured variants derived from nimotuzumab keep the original fine specificity and exhibit superior biological activity
Cited by: 6
Author(s): Yaima Tundidor, Luis F. Ponce, Lisset Chao, J Solozabal, Michael Hust, Stefan Dübel, Gertrudis Rojas
Software Mentions: 2
Published: almost 5 years ago