pypi: pymbar | Projects | Ecosyste.ms: Papers

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: over 2 years ago
6 dependent packages
2,022 downloads last month

Enhanced Analysis

Educational Contributors: lnaden@vt.edu michael.shirts@virginia.edu tburgin@umich.edu schuh.marc@students.boku.ac.at jbarnet4@tulane.edu chrisjones4@u.boisestate.edu

Repository Activity:

Repository Owner: Chodera lab // Memorial Sloan Kettering Cancer Center (organization) Academic

README Analysis: DOI Found

Science Score: 100/100

Starting Score: 100 points

Bonuses:

+120 Educational commit emails
6 contributors with educational email addresses
+20 Academic repository owner
Repository owned by academic institution
+15 Institutional repository owner
Repository owned by research institution
+24 Science terms in README
12 scientific terms found in README
+20 DOI references
2 DOI references found in README

Penalties:

-10 PyPI ecosystem
General-purpose ecosystem
-10 No science terms in description
No scientific terms found in description

Very Likely Science (100)

Papers Mentioning pymbar 12

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution
Cited by: 12
Author(s): Marcus Wieder, Josh Fass, John D. Chodera
Software Mentions: 4
Published: about 5 years ago

10.1002/jcc.26035

Force‐field parametrization based on radial and energy distribution functions
Cited by: 1
Author(s): Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi
Software Mentions: 3
Published: over 6 years ago

10.3389/fmolb.2021.712085

Recent Developments in Free Energy Calculations for Drug Discovery
Cited by: 39
Author(s): Edward J. King, Erick Aitchison, Han Li, Ray Luo
Software Mentions: 2
Published: over 4 years ago

10.1016/j.cell.2021.01.034

Antidepressant drugs act by directly binding to TRKB neurotrophin receptors
Cited 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: about 5 years ago

10.1039/c5sc02678d

Accurate calculation of the absolute free energy of binding for drug molecules
Cited by: 229
Author(s): Matteo Aldeghi, Alexander Heifetz, Michael J. Bodkin, S. Knapp, Philip C. Biggin
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-018-23778-5

On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation
Cited by: 17
Author(s): Giulia Pagani, Holger Gohlke
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0113119

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
Cited by: 13
Author(s): Andrew T. Fenley, Hari S. Muddana, Michael K. Gilson
Software Mentions: 1
Published: about 11 years ago

10.1021/acs.jpca.1c03454

Complex Reaction Network Thermodynamic and Kinetic Autoconstruction Based on Ab Initio Statistical Mechanics: A Case Study of O2 Activation on Ag4 Clusters
Cited by: 3
Author(s): Weiqi Wang, Xiangyue Liu, Jesús Pérez‐Ríos
Software Mentions: 1
Published: over 4 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: about 5 years ago

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