cran: bio3d | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0243927

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago

10.3390/e23010072

Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel
Cited by: 2
Author(s): Salvatore M. Cosseddu, Eunju Julia Choe, I. A. Khovanov
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pbio.3000301

Proteome-wide analysis of chaperone-mediated autophagy targeting motifs
Cited by: 125
Author(s): Philipp Kirchner, Mathieu Bourdenx, Julio Madrigal‐Matute, Simoni Tiano, Antonio Díaz, Boris Bartholdy, Britta Will, Ana María Cuervo
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-11-199

BioPhysConnectoR: Connecting Sequence Information and Biophysical Models
Cited by: 21
Author(s): Franziska Hoffgaard, Philipp Weil, Kay Hamacher
Software Mentions: 6
Published: over 14 years ago

10.1371/journal.pone.0052884

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
Cited by: 17
Author(s): Mark L. Grimes, Wan-Jui Lee, Laurens van der Maaten, Paul Shannon
Software Mentions: 6
Published: over 11 years ago

10.1186/1471-2164-13-531

Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei
Cited by: 57
Author(s): Oscar Franzén, Carlos Talavera-López, Stephen Ochaya, Claire E. Butler, Louisa A. Messenger, Michael D. Lewis, Martin S. Llewellyn, C. J. Marinkelle, Kevin M. Tyler, Michael A. Miles, Björn Andersson
Software Mentions: 5
Published: over 12 years ago

10.1101/2021.03.17.435863

Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies
Cited by: 31
Author(s): Allison J Greaney, Tyler N Starr, Christopher O. Barnes, Yiska Weisblum, Fabian Schmidt, Marina Caskey, Christian Gaebler, Alice Cho, Marianna Agudelo, Shlomo Finkin, Zijun Wang, Daniel Poston, Frauke Muecksch, Théodora Hatziioannou, Paul D. Bieniasz, Davide F. Robbiani, Michel C. Nussenzweig, Pamela J. Björkman, Jesse D. Bloom
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0058804

A Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 Genomes
Cited by: 7
Author(s): Yan Wang, Reda Rawi, Christoph Wilms, Dominik Heider, Rongge Yang, Daniel Hoffmann
Software Mentions: 4
Published: over 11 years ago

10.1074/jbc.RA119.011010

Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism
Cited by: 8
Author(s): Kenneth C Childers, Xin‐Qiu Yao, Sam Giannakoulias, Joshua Amason, Donald Hamelberg, Elsa D. Garcin
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0010588

Rhinovirus Genome Evolution during Experimental Human Infection
Cited by: 50
Author(s): Samuel Cordey, Thomas Junier, Daniel Gerlach, Francesca Gobbini, Laurent Farinelli, Evgeny M. Zdobnov, Birgit Winther, Caroline Tapparel, Laurent Kaiser
Software Mentions: 3
Published: over 14 years ago

10.1074/jbc.M116.770545

A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPLX Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding
Cited by: 16
Author(s): Patrick R. Blackburn, Alexander Tischer, Michael T. Zimmermann, Jennifer L. Kemppainen, Sujatha Sastry, Amy E. Knight Johnson, Margot A. Cousin, Nicole J. Boczek, Gavin R. Oliver, Vinod K. Misra, Ralitza H. Gavrilova, Gwen Lomberk, Matthew Auton, Raúl Urrutia, Eric W. Klee
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-9-109

Evolutionary Pareto-optimization of stably folding peptides
Cited by: 24
Author(s): Wolfram Gronwald, Tim Hohm, Daniel Hoffmann
Software Mentions: 2
Published: over 16 years ago

10.1007/s00249-020-01480-7

Inferring functional units in ion channel pores via relative entropy
Cited by: 1
Author(s): Michael Schmidt, Indra Schroeder, Daniel Bauer, Gerhard Thiel, Kay Hamacher
Software Mentions: 2
Published: over 3 years ago

10.1038/srep11550

RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens
Cited by: 3
Author(s): Luigi Grassi, Guido Leoni, Anna Tramontano
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2018.00276

Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties
Cited by: 11
Author(s): Michael T. Zimmermann, Raúl Urrutia, Margot A. Cousin, Gavin R. Oliver, Eric W. Klee
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0032071

The Influence of Coastal Access on Isotope Variation in Icelandic Arctic Foxes
Cited by: 23
Author(s): Fredrik Dalerum, Anna Perbro, Rannveig Magnúsdóttir, Páll Hersteinsson, Anders Angerbjörn
Software Mentions: 2
Published: over 12 years ago

10.1016/j.celrep.2020.108602

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases
Cited by: 20
Author(s): David Bradley, Cristina Viéitez, Vinothini Rajeeve, Joel Selkrig, Pedro R. Cutillas, Pedro Beltrão
Software Mentions: 2
Published: over 3 years ago

10.1093/ve/veaa085

HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification
Cited by: 4
Author(s): Nicolaas Christiaan Kist, Ben Lambert, Samuel Campbell, Aris Katzourakis, Daniel Lunn, Philippe Lemey, Astrid K. N. Iversen
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-49337-0

MARK4 protein can explore the active-like conformations in its non-phosphorylated state
Cited by: 4
Author(s): Sajjad Ahrari, Fatemeh Khosravi, Ali Osouli, Amirhossein Sakhteman, Alireza Nematollahi, Younes Ghasemi, Amir Savardashtaki
Software Mentions: 1
Published: about 5 years ago

10.1155/2017/7263780

Novel Pathogenic Variant in TGFBR2 Confirmed by Molecular Modeling Is a Rare Cause of Loeys-Dietz Syndrome
Cited by: 2
Author(s): Michael T. Zimmermann, Raúl Urrutia, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Eric W. Klee, Colleen Macmurdo, Paldeep S. Atwal
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0147240

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes
Cited by: 17
Author(s): Dhanusha Yesudhas, Muhammad Ayaz Anwar, Paladugu Suresh, Prasannavenkatesh Durai, Masaud Shah, Sangdun Choi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0042671

Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies
Cited by: 78
Author(s): Sotirios Vasileiadis, Edoardo Puglisi, Maria Arena, Fabrizio Cappa, Pier Sandro Cocconcelli, Marco Trevisan
Software Mentions: 1
Published: about 12 years ago

10.3390/biom9110706

Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization
Cited by: 6
Author(s): Pedro R. Magalhães, Miguel Machuqueiro, José Guilherme de Andrade Almeida, André Melo, M. Natália D. S. Cordeiro, Sandra Cabo Verde, Zeynep H. Gümüş, Irina S. Moreira, João D. G. Correia, Rita Melo
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmolb.2021.740904

The Role of Substrate Mediated Allostery in the Catalytic Competency of the Bacterial Oligosaccharyltransferase PglB
Cited by: 0
Author(s): Brittany R. Morgan, Francesca Massi
Software Mentions: 1
Published: about 3 years ago

10.1186/s13027-017-0155-4

Whole-genome analysis of human papillomavirus genotypes 52 and 58 isolated from Japanese women with cervical intraepithelial neoplasia and invasive cervical cancer
Cited by: 16
Author(s): Yuri Tenjimbayashi, Mamiko Onuki, Yusuke Hirose, Shuji Mori, Yoshiyuki Ishii, Takamasa Takeuchi, Nobutaka Tasaka, Toyomi Satoh, Tohru Morisada, Takashi Iwata, Shingo Miyamoto, Koji Matsumoto, Akihiko Sekizawa, Iwao Kukimoto
Software Mentions: 1
Published: about 7 years ago

10.1074/jbc.REV120.013745

Building better polymerases: Engineering the replication of expanded genetic alphabets
Cited by: 13
Author(s): Zahra Ouaray, Steven A. Benner, Millie M. Georgiadis, Nigel G. J. Richards
Software Mentions: 1
Published: almost 4 years ago

10.1038/srep45053

Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen
Cited by: 26
Author(s): Lorenzo Di Rienzo, Edoardo Milanetti, Rosalba Lepore, Pier Paolo Olimpieri, Anna Tramontano
Software Mentions: 1
Published: over 7 years ago

Ecosyste.ms: Papers

Projects: cran: bio3d

Papers Mentioning bio3d 27