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: propka
https://packages.ecosyste.ms/registries/pypi.org/packages/propka
Heuristic pKa calculations with ligands
5 versions
Latest release: almost 2 years ago
3 dependent packages
2,155 downloads last month
Papers Mentioning propka 15
10.3389/fmicb.2021.720991
The Role of Hydrophobic Nodes in the Dynamics of Class A β-LactamasesCited by: 5
Author(s): Edgar Olehnovics, Junqi Yin, Adrià Pérez, Gianni De Fabritiis, Robert A. Bonomo, Debsindhu Bhowmik, Shozeb Haider
Software Mentions: 5
Published: about 3 years ago
10.1111/j.1747-0285.2011.01101.x
Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand‐bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial TargetCited by: 37
Author(s): William Sinko, César de Oliveira, S. Williams, Adam Van Wynsberghe, Jacob D. Durrant, Rong Cao, Eric Oldfield, J. Andrew McCammon
Software Mentions: 4
Published: over 13 years ago
10.3389/fmolb.2021.720561
Exploring Ligand Binding to Calcitonin Gene-Related Peptide ReceptorsCited by: 5
Author(s): Giuseppe Deganutti, Silvia Atanasio, Roxana Maria Rujan, Patrick M. Sexton, Denise Wootten, Christopher A. Reynolds
Software Mentions: 4
Published: about 3 years ago
10.1016/j.bcp.2018.02.005
Extracellular loops 2 and 3 of the calcitonin receptor selectively modify agonist binding and efficacyCited by: 24
Author(s): Emma Dal Maso, Yue Zhu, Vi Pham, Christopher A. Reynolds, Giuseppe Deganutti, Caroline A. Hick, Dehua Yang, Arthur Christopoulos, Debbie L. Hay, Ming Wei Wang, Patrick M. Sexton, Sebastian G.B. Furness, Denise Wootten
Software Mentions: 3
Published: over 6 years ago
10.1111/febs.13208
‘Dopamine‐first’ mechanism enables the rational engineering of the norcoclaurine synthase aldehyde activity profileCited by: 60
Author(s): Benjamin R. Lichman, Markus Gershater, Eleanor D. Lamming, Thomas Pesnot, Altin Sula, Nicholas H. Keep, Helen C. Hailes, John M. Ward
Software Mentions: 3
Published: almost 10 years ago
10.1074/jbc.RA120.016004
Dissecting the low catalytic capability of flavin-dependent halogenasesCited by: 21
Author(s): Aisaraphon Phintha, Kridsadakorn Prakinee, A. Jaruwat, Narin Lawan, Surawit Visitsatthawong, Chadaporn Kantiwiriyawanitch, Warangkhana Songsungthong, Duangthip Trisrivirat, Pirom Chenprakhon, Adrian J. Mulholland, Karl‐Heinz van Pée, P. Chitnumsub, Pimchai Chaiyen
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-018-29871-z
Insight into the molecular mechanism behind PEG-mediated stabilization of biofluid lipasesCited by: 13
Author(s): Bianca Pérez, Andrea Coletta, Jannik Nedergaard Pedersen, Steen V. Petersen, Xavier Periole, Richard B. Sessions, Zheng Guo, Adam W. Perriman, Birgit Schiøtt
Software Mentions: 2
Published: over 6 years ago
10.1186/s12900-015-0038-0
Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics studyCited by: 4
Author(s): Javier Cáceres-Delpiano, Jaime Teneb, Ricardo Mansilla, Antonio Manuel Rodríguez García, Alexis Salas-Burgos
Software Mentions: 1
Published: over 9 years ago
10.7554/eLife.69482
The fluoride permeation pathway and anion recognition in Fluc family fluoride channelsCited by: 5
Author(s): Benjamin McIlwain, Roja Gundepudi, B Ben Koff, Randy B. Stockbridge
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules26133986
Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double StrandCited by: 5
Author(s): Cécilia Hognon, Antonio Monari
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules26010239
Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD SimulationCited by: 1
Author(s): Shalini Yadav, Vishnudatt Pandey, Rakesh Tiwari, Rajendra Prasad Ojha, Kshatresh Dutta Dubey
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0059797
Structure Based Descriptors for the Estimation of Colloidal Interactions and Protein Aggregation PropensitiesCited by: 12
Author(s): Michael Brunsteiner, Michaela Flock, Bernd Nidetzky
Software Mentions: 1
Published: over 11 years ago
10.1002/2211-5463.12441
Bioinformatic analysis of the fold type I <scp>PLP</scp> ‐dependent enzymes reveals determinants of reaction specificity in <scp>l</scp> ‐threonine aldolase from <i>Aeromonas jandaei</i>Cited by: 28
Author(s): Kateryna Fesko, Dmitry A. Suplatov, Vytas K. Švedas
Software Mentions: 1
Published: over 6 years ago
10.3389/fmolb.2020.00170
Evidence for Disruption of Mg2+ Pair as a Resistance Mechanism Against HIV-1 Integrase Strand Transfer InhibitorsCited by: 1
Author(s): Lucas de Almeida Machado, Ana Carolina Ramos Guimarães
Software Mentions: 1
Published: over 4 years ago
10.1038/srep13264
Less is More: Design of a Highly Stable Disulfide-Deleted Mutant of Analgesic Cyclic α-Conotoxin Vc1.1Cited by: 41
Author(s): Rilei Yu, Victoria A. L. Seymour, Géza Berecki, Xinying Jia, Muharrem Akcan, David J. Adams, Quentin Kaas, David J. Craik
Software Mentions: 1
Published: over 9 years ago