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: pymbar
https://packages.ecosyste.ms/registries/pypi.org/packages/pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR) method
13 versions
Latest release: about 1 year ago
6 dependent packages
2,022 downloads last month
Papers Mentioning pymbar 12
10.1039/d1sc01185e
Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solutionCited by: 12
Author(s): Marcus Wieder, Josh Fass, John D. Chodera
Software Mentions: 4
Published: over 3 years ago
10.1002/jcc.26035
Force‐field parametrization based on radial and energy distribution functionsCited by: 1
Author(s): Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi
Software Mentions: 3
Published: about 5 years ago
10.3389/fmolb.2021.712085
Recent Developments in Free Energy Calculations for Drug DiscoveryCited by: 39
Author(s): Edward J. King, Erick Aitchison, Han Li, Ray Luo
Software Mentions: 2
Published: about 3 years ago
10.1016/j.cell.2021.01.034
Antidepressant drugs act by directly binding to TRKB neurotrophin receptorsCited by: 275
Author(s): Plínio Casarotto, Mykhailo Girych, Senem Merve Fred, Vera Kovaleva, Rafael Moliner, Giray Enkavi, Caroline Biojone, Cecilia Cannarozzo, Madhusmita Priyadarshini Sahu, Katja Kaurinkoski, Cecilia A. Brunello, Anna Steinzeig, Frederike Winkel, Sudarshan Patil, Stefan Vestring, Tsvetan Serchov, Cassiano Ricardo Alves Faria Diniz, Liina Laukkanen, Iseline Cardon, Hanna Antila, Tomasz Róg, Petteri Piepponen, Clive R. Bramham, Claus Normann, Sari E. Lauri, Märt Saarma, Ilpo Vattulainen, Eero Ċastrén
Software Mentions: 2
Published: over 3 years ago
10.1039/c5sc02678d
Accurate calculation of the absolute free energy of binding for drug moleculesCited by: 229
Author(s): Matteo Aldeghi, Alexander Heifetz, Michael J. Bodkin, S. Knapp, Philip C. Biggin
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-018-23778-5
On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activationCited by: 17
Author(s): Giulia Pagani, Holger Gohlke
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0113119
Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and BiomoleculesCited by: 13
Author(s): Andrew T. Fenley, Hari S. Muddana, Michael K. Gilson
Software Mentions: 1
Published: almost 10 years ago
10.1021/acs.jpca.1c03454
Complex Reaction Network Thermodynamic and Kinetic Autoconstruction Based on <i>Ab Initio</i> Statistical Mechanics: A Case Study of O<sub>2</sub> Activation on Ag<sub>4</sub> ClustersCited by: 3
Author(s): Weiqi Wang, Xiangyue Liu, Jesús Pérez‐Ríos
Software Mentions: 1
Published: over 3 years ago
10.3389/fmolb.2021.661322
Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin.Cited by: 3
Author(s): Jules Nde, Pengzhi Zhang, Jacob C. Ezerski, Wei Lu, Kaitlin Knapp, Peter G. Wolynes, Margaret S. Cheung
Software Mentions: 1
Published: over 3 years ago
10.1007/s10822-017-0056-z
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and dockingCited by: 9
Author(s): Martin Olsson, Alfonso T. García-Sosa, Ulf Ryde
Software Mentions: 1
Published: about 7 years ago
10.1007/s10822-016-9969-1
Blinded predictions of distribution coefficients in the SAMPL5 challengeCited by: 13
Author(s): Stefano Bosisio, Antonia S. J. S. Mey, Julien Michel
Software Mentions: 1
Published: almost 8 years ago
10.1007/s10822-017-0083-9
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculationsCited by: 18
Author(s): Antonia S. J. S. Mey, Jordi Jiménez, Julien Michel
Software Mentions: 1
Published: almost 7 years ago