Ecosyste.ms: Papers

10.1186/1472-6807-9-27

PTools: an opensource molecular docking library
Cited by: 34
Author(s): Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
Software Mentions: 9
Published: over 15 years ago

10.1093/bib/bbaa150

Recent advances in user-friendly computational tools to engineer protein function
Cited by: 30
Author(s): Carlos Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-12-61

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines
Cited by: 10
Author(s): Marcin Cieślik, Cameron Mura
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2105-8-232

TMM@: a web application for the analysis of transmembrane helix mobility
Cited by: 2
Author(s): Lars Skjærven, Inge Jonassen, Nathalie Reuter
Software Mentions: 4
Published: about 17 years ago

10.3390/biom10040527

Aspirin: A Suicide Inhibitor of Carbonic Anhydrase II
Cited by: 10
Author(s): Jacob T. Andring, Jacob Combs, Robert McKenna
Software Mentions: 4
Published: over 4 years ago

10.1016/j.dib.2016.01.016

Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor
Cited by: 5
Author(s): Nitin Chitranshi, Vivek Kumar Gupta, Yogita Dheer, Veer Bala Gupta, Roshana Vander Wall, Stuart L. Graham
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-6-52

Cited by: 105
Author(s): Siv Midtun Hollup, Gisle Salensminde, Nathalie Reuter
Software Mentions: 3
Published: over 19 years ago

10.1590/0074-02760200179

Coagulation modifiers targeting SARS-CoV-2 main protease Mpro for COVID-19 treatment: an in silico approach
Cited by: 18
Author(s): Ísis Venturi Biembengut, Tatiana de Arruda Campos Brasil de Souza
Software Mentions: 2
Published: over 4 years ago

10.3390/jcm10030465

Tumor Necrosis Factor Receptor-Associated Periodic Syndrome (TRAPS) with a New Pathogenic Variant in TNFRSF1A Gene in a Family of the Adult Male with Renal AA Amyloidosis—Diagnostic and Therapeutic Challenge for Clinicians
Cited by: 2
Author(s): Jolanta Żegarska, Ewa Więsik-Szewczyk, Ewa Hryniewiecka, Beata Wolska-Kuśnierz, Dariusz Sołdacki, Magdalena M. Kacprzak, Agnieszka Sobczyńska-Tomaszewska, Kamila Czerska, Paweł Siedlecki, Karina Jahnz-Różyk, Ewa Bernatowska, Radosław Zagożdżon, Leszek Pączek
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1006325

A model for hydrophobic protrusions on peripheral membrane proteins
Cited by: 22
Author(s): Edvin Fuglebakk, Nathalie Reuter
Software Mentions: 2
Published: about 6 years ago

10.1038/srep22148

Fast antibody fragment motion: flexible linkers act as entropic spring
Cited by: 25
Author(s): Laura R. Stingaciu, Oxana Ivanova, Michael Ohl, Ralf Biehl, D. Richter
Software Mentions: 2
Published: over 8 years ago

10.1186/s13104-021-05536-5

libxtc: an efficient library for reading XTC-compressed MD trajectory data
Cited by: 9
Author(s): Н. А. Крылов, Roman G. Efremov
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1000389

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
Cited by: 51
Author(s): Javad Golji, Ruth Collins, Mohammad R. K. Mofrad
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0009613

Evolutionary Constraints Acting on DDX3X Protein Potentially Interferes with Rev-Mediated Nuclear Export of HIV-1 RNA
Cited by: 10
Author(s): Deepak Sharma, Jayanta Bhattacharya
Software Mentions: 1
Published: over 14 years ago

10.3389/fmolb.2019.00089

Mapping of a Regulatory Site of the Escherichia coli ADP-Glucose Pyrophosphorylase
Cited by: 9
Author(s): Jaina A Bhayani, Benjamin L. Hill, Anisha Sharma, Alberto A. Iglesias, Kenneth W. Olsen, Miguel A. Ballícora
Software Mentions: 1
Published: almost 5 years ago

10.1002/jcc.21688

Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Cited by: 225
Author(s): Michele Seeber, Angelo Felline, Francesco Raimondi, Stefanie Muff, Ran Friedman, Francesco Rao, Amedeo Caflisch, Francesca Fanelli
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-020-57775-4

Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
Cited by: 8
Author(s): Livia Balacescu, Tobias E. Schrader, Aurel Rădulescu, Piotr Zolnierczuk, Olaf Holderer, Stefano Pasini, Jörg Fitter, Andreas Stadler
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-11-363

Robust probabilistic superposition and comparison of protein structures
Cited by: 12
Author(s): Martin Mechelke, Michael Habeck
Software Mentions: 1
Published: about 14 years ago

10.1107/S2052252518001021

Crystal structures of<i>Lymphocytic choriomeningitis virus</i>endonuclease domain complexed with diketo-acid ligands
Cited by: 12
Author(s): Magalí Sáez‐Ayala, Elsie Laban Yekwa, Mauro Carcelli, Bruno Canard, Karine Alvarez, François Ferrón
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-14-183

Δ ΔPT: a comprehensive toolbox for the analysis of protein motion
Cited by: 21
Author(s): Thomas L. Rodgers, David Burnell, Phil D. Townsend, Ehmke Pohl, Martin J. Cann, Mark R. Wilson, Tom McLeish
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-11-352

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation
Cited by: 11
Author(s): Albert Solernou, Juan Fernández‐Recio
Software Mentions: 1
Published: about 14 years ago

10.1186/s13628-016-0032-3

Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding
Cited by: 14
Author(s): Clemens Sill, Ralf Biehl, Bernd Hoffmann, Aurel Rădulescu, Marie‐Sousai Appavou, B. Faragó, Rudolf Merkel, D. Richter
Software Mentions: 1
Published: almost 8 years ago

10.3390/molecules14093436

The Use of MoStBioDat for Rapid Screening of Molecular Diversity
Cited by: 4
Author(s): Andrzej Bąk, Jarosław Polański, Agata Kurczyk
Software Mentions: 1
Published: about 15 years ago

10.7717/peerj.6012

Steroidal glycoalkaloids from<i>Solanum nigrum</i>target cytoskeletal proteins: an<i>in silico</i>analysis
Cited by: 18
Author(s): Rumana Ahmad
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1002301

Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication
Cited by: 44
Author(s): Simon Mitternacht, Igor N. Berezovsky
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1002148

Binding Leverage as a Molecular Basis for Allosteric Regulation
Cited by: 77
Author(s): Simon Mitternacht, Igor N. Berezovsky
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pcbi.1002948

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
Cited by: 33
Author(s): Mehrdad Mehrbod, Mohammad R. K. Mofrad
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1004678

Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication
Cited by: 98
Author(s): Enrico Guarnera, Igor N. Berezovsky
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1006228

Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response
Cited by: 61
Author(s): Wei-Ven Tee, Enrico Guarnera, Igor N. Berezovsky
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1007782

Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae
Cited by: 10
Author(s): Weimin Wu, Norman R. Watts, Naiqian Cheng, Rick Huang, Alasdair C. Steven, Paul T. Wingfield
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0150267

Monomeric Amyloid Beta Peptide in Hexafluoroisopropanol Detected by Small Angle Neutron Scattering
Cited by: 30
Author(s): Bo Zhang-Haagen, Ralf Biehl, Luitgard Nagel-Steger, Aurel Rădulescu, D. Richter, Dieter Willbold
Software Mentions: 1
Published: over 8 years ago