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: pdb2pqr
https://packages.ecosyste.ms/registries/pypi.org/packages/pdb2pqr
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.
15 versions
Latest release: over 1 year ago
2 dependent packages
2,176 downloads last month
Papers Mentioning pdb2pqr 41
10.1371/journal.pone.0100736
Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable RegionsCited by: 125
Author(s): Jasmin F. Sydow, Florian Lipsmeier, Vincent Larraillet, Maximiliane Hilger, Bjoern Mautz, Michael Mølhøj, Jan Kuentzer, Stefan Klostermann, Juergen Schoch, Hans R. Voelger, Jörg T. Regula, Patrick Cramer, Apollon Papadimitriou, Hubert Kettenberger
Software Mentions: 5
Published: over 10 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.str.2011.03.023
Insights into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13Cited by: 79
Author(s): Mohammad W. Bahar, Stephen C. Graham, David I. Stuart, Jonathan M. Grimes
Software Mentions: 4
Published: over 13 years ago
10.3390/molecules25245934
CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics SimulationsCited by: 13
Author(s): Alessandro Marchetto, Zeineb Si Chaib, Claudia Rossi, Rui P. P. L. Ribeiro, Sergio Pantano, Giulia Rossetti, Alejandro Giorgetti
Software Mentions: 4
Published: almost 4 years ago
10.3390/v11080691
Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 ProteaseCited by: 1
Author(s): Allan Peres-da-Silva, Deborah Antunes, Audálio Rebelo Torres, Ernesto R. Caffarena, Elisabeth Lampe
Software Mentions: 3
Published: over 5 years ago
10.3390/md18070349
Interactions of the α3β2 Nicotinic Acetylcholine Receptor Interfaces with α-Conotoxin LsIA and its Carboxylated C-terminus Analogue: Molecular Dynamics SimulationsCited by: 3
Author(s): Jierong Wen, David J. Adams, Andrew Hung
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-48849-z
Modelling of substrate access and substrate binding to cephalosporin acylasesCited by: 6
Author(s): Virgilio F. Ferrario, Mona Fischer, Yushan Zhu, Jürgen Pleiss
Software Mentions: 3
Published: about 5 years ago
10.1186/1471-2164-15-S9-S2
TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancerCited by: 60
Author(s): Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi
Software Mentions: 3
Published: almost 10 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
10.3390/ijms20133121
Unveiling the Interplay between the TLR4/MD2 Complex and HSP70 in the Human Cardiovascular System: A Computational ApproachCited by: 18
Author(s): Amanda Almeida de Oliveira, Josemar Faustino, Maria Elena de Lima, Ronaldo Menezes, Kênia Pedrosa Nunes
Software Mentions: 2
Published: over 5 years ago
10.3390/biom10091330
Allosteric Inhibition of Adenylyl Cyclase Type 5 by G-Protein: A Molecular Dynamics StudyCited by: 7
Author(s): Elisa Frezza, Tina-Méryl Amans, Juliette Martin
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0063730
Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile PredictionCited by: 18
Author(s): Stéphanie Pérot, Leslie Regad, Christelle Reynès, Olivier Spérandio, Maria A. Miteva, Bruno O. Villoutreix, Anne-Claude Camproux
Software Mentions: 2
Published: over 11 years ago
10.12688/f1000research.10541.3
A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modelingCited by: 4
Author(s): Dmitrii M. Nikolaev, Emil Anton, В. М. Бойцов, Maxim S. Panov, Mikhail N. Ryazantsev
Software Mentions: 2
Published: about 7 years ago
10.3389/fmolb.2021.716466
SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular DockingCited by: 17
Author(s): Samuel Murail, Sjoerd J. de Vries, Julien Rey, Gautier Moroy, Pierre Tufféry
Software Mentions: 2
Published: about 3 years ago
10.1074/jbc.RA120.016350
Functional metagenomics of the thioredoxin superfamilyCited by: 6
Author(s): Sebastian Nilewski, Marharyta Varatnitskaya, Thorsten Masuch, Anna Kusnezowa, Manuela Gellert, Anne F Baumann, Natalie Lupilov, Witali Kusnezow, Markus-Hermann Koch, Martin Eisenacher, Mehmet Berkmen, Christopher Horst Lillig, Lars I. Leichert
Software Mentions: 2
Published: almost 4 years ago
10.1007/s13238-018-0518-7
Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferaseCited by: 78
Author(s): Jinbo Huang, Dongyan Xu, Zhou Gong, Ling-Yun Qin, Shuai Yang, Yue-Ling Zhu, Xiang Wang, Delin Zhang, Tingting Zou, Ping Yin, Chun Tang
Software Mentions: 2
Published: over 6 years ago
10.1038/srep17356
Conservation and Role of Electrostatics in Thymidylate SynthaseCited by: 7
Author(s): Divita Garg, Stéphane Skouloubris, Julien Briffotaux, Hannu Myllykallio, Rebecca C. Wade
Software Mentions: 2
Published: almost 9 years ago
10.1038/s41598-017-16392-4
Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycanCited by: 22
Author(s): Noemí Bustamante, Manuel Iglesias-Bexiga, N. Bernardo-García, N. Silva-Martin, Gema Alejandra Botana García, María Asunción Campanero-Rhodes, Esther Perez Garcia, Isabel Usón, Rubén M. Buey, Pedro Garcı́a, J.A. Hermoso, Marta Bruix, Margarita Menéndez
Software Mentions: 2
Published: almost 7 years ago
10.18632/oncotarget.26136
Molecular dynamics simulation reveals the possible druggable<i>hot-spots</i>of USP7Cited by: 29
Author(s): Mitul Srivastava, Charu Suri, Mrityunjay Singh, Rajani Mathur, Shailendra Asthana
Software Mentions: 2
Published: about 6 years ago
10.3390/biom11081104
Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics ApproachesCited by: 2
Author(s): Rafał Madaj, Bartłomiej Gostyński, Róża Pawłowska, Arkadiusz Chworoś
Software Mentions: 1
Published: over 3 years ago
10.3390/ijms21103659
Identification of Inhibitors to Trypanosoma cruzi Sirtuins Based on Compounds Developed to Human EnzymesCited by: 8
Author(s): Tanira Matutino Bastos, Milena Botelho Pereira Soares, Caio Haddad Franco, Laura Maria Alcântara, Lorenzo Antonini, Manuela Sabatino, Nicola Mautone, Lúcio H. Freitas‐Junior, Carolina Borsoi Moraes, Rino Ragno, Dante Rotili, Sérgio Schenkman, Antonello Mai, Nilmar Silvio Moretti
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms21186669
Interaction Modes of Microsomal Cytochrome P450s with Its Reductase and the Role of Substrate BindingCited by: 7
Author(s): Francisco Esteves, Philippe Urban, José Rueff, Gilles Truan, Michel Kranendonk
Software Mentions: 1
Published: about 4 years ago
10.1039/c7ra12799e
A multi-scale approach to describe electrical impulses propagating along actin filaments in both intracellular and<i>in vitro</i>conditionsCited by: 27
Author(s): Christian Hunley, Diego Uribe, Marcelo Marucho
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12977-014-0130-8
Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activitiesCited by: 32
Author(s): Mithun Mitra, Dustin Singer, Yu Mano, Jozef Hritz, Gabriel Nam, Robert J. Gorelick, In‐Ja L. Byeon, Angela M. Gronenborn, Yoshinori Iwatani, Joseph Levin
Software Mentions: 1
Published: almost 10 years ago
10.1126/sciadv.1602937
Homeodomain-like DNA binding proteins control the haploid-to-diploid transition in <i>Dictyostelium</i>Cited by: 21
Author(s): Katy Hedgethorne, Sebastian Eustermann, Ji‐Chun Yang, T.E.H. Ogden, David Neuhaus, Gareth Bloomfield
Software Mentions: 1
Published: about 7 years ago
10.1126/sciadv.aba4897
Structure and assembly of ESCRT-III helical Vps24 filamentsCited by: 28
Author(s): Stefan T. Huber, Siavash Mostafavi, Simon A. Mortensen, Carsten Sachse
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms22063029
Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band MaximaCited by: 8
Author(s): Andrey A. Shtyrov, Dmitrii M. Nikolaev, Vladimir N. Mironov, А. В. Васин, Maxim S. Panov, Yu. S. Tver’yanovich, Mikhail N. Ryazantsev
Software Mentions: 1
Published: over 3 years ago
10.1038/srep24191
Architectural plasticity of AMPK revealed by electron microscopy and X-ray crystallographyCited by: 3
Author(s): Yan Ouyang, Li Zhu, Yi-Fang Li, Miaomiao Guo, Yang Liu, Jin Cheng, Jing Zhao, Yi Wu
Software Mentions: 1
Published: over 8 years ago
10.1038/srep38259
On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexesCited by: 10
Author(s): Guillaume Copie, Fabrizio Cleri, Ralf Blossey, Marc F. Lensink
Software Mentions: 1
Published: almost 8 years ago
10.1155/2021/6621292
Molecular Basis for the Interactions of Human Thioredoxins with Their Respective ReductasesCited by: 6
Author(s): Faruq Hossain, Yana Bodnar, Calvin Klein, Clara Ortegón Salas, Elias S.J. Arnér, Manuela Gellert, Christopher Horst Lillig
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pcbi.1002777
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation StudyCited by: 36
Author(s): Peter M. Kekenes‐Huskey, Steffen Lindert, J. Andrew McCammon
Software Mentions: 1
Published: almost 12 years ago
10.1038/s41598-019-51942-y
Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics StudyCited by: 13
Author(s): Nathalie Basdevant, Delphine Dessaux, Rosa Ramirez
Software Mentions: 1
Published: about 5 years ago
10.1111/bph.13214
Mechanism of inhibition of mouse <scp>S</scp> lo3 ( <scp>K</scp> <sub>Ca</sub> 5.1) potassium channels by quinine, quinidine and bariumCited by: 17
Author(s): David C. Wrighton, Stephen P. Muench, Jonathan D. Lippiat
Software Mentions: 1
Published: over 9 years ago
10.3390/ijms19051383
Molecular Surface Remeshing with Local Region RefinementCited by: 7
Author(s): Dawar Khan, Dong‐Ming Yan, Sheng Gui, Benzhuo Lu, Xiaopeng Zhang
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0112351
Phospholipase A2 Isolated from the Venom of Crotalus durissus terrificus Inactivates Dengue virus and Other Enveloped Viruses by Disrupting the Viral EnvelopeCited by: 50
Author(s): Vanessa Danielle Menjon Müller, Ricardo Oliveira dos Santos Soares, Nilton Nascimento Santos-Júnior, Amanda Cristina Trabuco, Adélia Cristina Oliveira Cintra, Luíz Tadeu Moraes Figueiredo, A. Caliri, Suely Vilela Sampaio, Víctor Hugo Aquino
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0152002
The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation StudyCited by: 5
Author(s): Lili Sun, Marcin Tabaka, Sen Hou, Lin Li, Krzysztof Burdzy, Aleksei Aksimentiev, Christopher Maffeo, Xuzhu Zhang, Robert Hołyst
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0196207
A molecular dynamics study of adenylyl cyclase: The impact of ATP and G-protein bindingCited by: 17
Author(s): Elisa Frezza, Juliette Martin, Richard Lavery
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0118940
Charge Reduction and Thermodynamic Stabilization of Substrate RNAs Inhibit RNA EditingCited by: 6
Author(s): Wolf-Matthias Leeder, Andreas J. Reuss, Michael Brecht, Katja Kratz, Josef Wachtveitl, H. Ulrich Göringer
Software Mentions: 1
Published: over 9 years ago
10.1111/cbdd.12121
Farnesyl Diphosphate Synthase Inhibitors from <i>In Silico</i> ScreeningCited by: 40
Author(s): Steffen Lindert, Wei Zhu, Yi Liang Liu, Ran Pang, Eric Oldfield, J. Andrew McCammon
Software Mentions: 1
Published: over 11 years ago
10.3390/ijms19071974
Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 EnzymesCited by: 14
Author(s): Verònica Postils, Maud Saint-André, Amy Timmins, Xiao Xi Li, Yong Wang, Josep M. Luis, Miquel Solà, Sam P. de Visser
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pntd.0002719
Deliberate Attenuation of Chikungunya Virus by Adaptation to Heparan Sulfate-Dependent Infectivity: A Model for Rational Arboviral Vaccine DesignCited by: 79
Author(s): Christina L. Gardner, Jozef Hritz, Chaoyang Sun, Dana L. Vanlandingham, Timothy Song, Elodie Ghedin, Stephen Higgs, William B. Klimstra, Kate D. Ryman
Software Mentions: 1
Published: almost 11 years ago