pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006237

Statistical investigations of protein residue direct couplings
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 1
Published: almost 6 years ago

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
Cited by: 44
Author(s): Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luís Serrano, Frédéric Rousseau, Joost Schymkowitz
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1003585

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors
Cited by: 59
Author(s): Lars Boukharta, Hugo Gutiérrez‐de‐Terán, Johan Åqvist
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1005787

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
Cited by: 23
Author(s): Gudrun Gygli, Fátima Lucas, Vı́ctor Guallar, Willem J.H. van Berkel
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pcbi.1002068

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
Cited by: 71
Author(s): Élodie Laine, Isaure Chauvot de Beauchêne, David Pérahia, Christian Auclair, Luba Tchertanov
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1000484

Computation of Conformational Coupling in Allosteric Proteins
Cited by: 50
Author(s): Brian Kidd, David Baker, Wendy E. Thomas
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pcbi.1000441

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
Cited by: 90
Author(s): Lun Yang, Jian Chen, Lin He
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1006511

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
Cited by: 23
Author(s): Ying‐Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing‐Ke Weng, Yi Wang
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1007193

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
Cited by: 14
Author(s): Bogdan Barz, Jennifer Loschwitz, Birgit Strodel
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1002103

Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases
Cited by: 19
Author(s): Michael D. Daily, George N. Phillips, Qiang Cui
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1006295

The permeation mechanism of organic cations through a CNG mimic channel
Cited by: 1
Author(s): L.M. Napolitano, Arin Marchesi, Álex Rodríguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1002128

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex
Cited by: 28
Author(s): A. Sofia F. Oliveira, António M. Baptista, Cláudio M. Soares
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1002754

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network
Cited by: 16
Author(s): Sjoerd J. L. van Wijk, Adrien Melquiond, Sjoerd J. de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.0020098

Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome
Cited by: 87
Author(s): Adrian H. Elcock
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.1002555

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Cited by: 84
Author(s): Yasuhiro Matsunaga, Hiroya Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1003718

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides
Cited by: 34
Author(s): James B. Smadbeck, Kiat Hwa Chan, George Khoury, Bin Xue, Robert Robinson, Charlotte Hauser, Christodoulos A. Floudas
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1000293

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
Cited by: 99
Author(s): Michael D. Daily, Jeffrey J. Gray
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pcbi.1004661

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
Cited by: 17
Author(s): Tatjana Braun, Julia Koehler Leman, Oliver Lange
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1000376

Prediction of Protein Binding Regions in Disordered Proteins
Cited by: 525
Author(s): Bálint Mészáros, István Simon, Zsuzsanna Dosztányi
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1006969

A global map of the protein shape universe
Cited by: 19
Author(s): Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1002646

The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles
Cited by: 11
Author(s): Deena M.A. Gendoo, Paul M. Harrison
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1007569

Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
Cited by: 38
Author(s): Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pcbi.1003253

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
Cited by: 55
Author(s): Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain Wallace, Vinod Kumar, Ursula Pieper, Andrej Šali, James R. Brown, John P. Overington, Marc A. Martí‐Renom
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.1000689

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease
Cited by: 21
Author(s): Neema L. Salimi, Bosco Ho, David A. Agard
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1002509

Dynamic Prestress in a Globular Protein
Cited by: 28
Author(s): Scott A. Edwards, J. Wagner, Frauke Gräter
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1000360

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Cited by: 126
Author(s): Zheng Yang, Peter Marynen, İvet Bahar
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1000668

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures
Cited by: 44
Author(s): Fred P. Davis, Andrej Šali
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1003249

Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
Cited by: 75
Author(s): Fan Jin, Yu Chen, Luhua Lai, Zhongfan Liu
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.1002016

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study
Cited by: 92
Author(s): Lun Yang, Kejian Wang, Jian Chen, Anil G. Jegga, Heng Luo, Leming Shi, Chunling Wan, Xiaolei Guo, Shengying Qin, Guang He, Feng Gao, Lin He
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1004548

Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains
Cited by: 18
Author(s): Anja Winter, Ralf Schmid, Richard Bayliss
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.1009009

Ten simple rules for designing analogue science games
Cited by: 1
Author(s): Sam Illingworth, Paul Wake
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1008818

Prediction of amphipathic helix—membrane interactions with Rosetta
Cited by: 3
Author(s): Alican Gulsevin, Jens Meiler
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1002682

Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
Cited by: 39
Author(s): Iskra Staneva, Yongqi Huang, Zhongfan Liu, Stefan Wallin
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1006126

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin
Cited by: 15
Author(s): Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.0030211

Detecting Coevolution in and among Protein Domains
Cited by: 157
Author(s): Chen Hsiang Yeang, David Haussler
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pcbi.1000056

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains
Cited by: 54
Author(s): Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1003901

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
Cited by: 13
Author(s): Kei Moritsugu, Tohru Terada, Akinori Kidera
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pcbi.1005826

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
Cited by: 17
Author(s): Shaima Hashem, Matteo Tiberti, Arianna Fornili
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pcbi.1008403

Ten simple rules for starting research in your late teens
Cited by: 0
Author(s): Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pcbi.1002869

Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore
Cited by: 65
Author(s): Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xianzhong Dai, Jianfeng Wang, Hongen Li, Xin Wang, Winson Jianhong Tan, Mingjing Luo, Xiaodi Niu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.0040043

Accurate Structural Correlations from Maximum Likelihood Superpositions
Cited by: 86
Author(s): Douglas L. Theobald, Deborah S. Wuttke
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pcbi.0020124

The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
Cited by: 107
Author(s): Wankyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pcbi.1002420

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB
Cited by: 35
Author(s): Elif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloğlu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1000627

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
Cited by: 56
Author(s): Menachem Fromer, Julia M. Shifman
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1000406

A Probabilistic Model of RNA Conformational Space
Cited by: 83
Author(s): Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff‐Borg, Thomas Hamelryck
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1008101

Quantitative profiling of protease specificity
Cited by: 5
Author(s): Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pcbi.1006458

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling
Cited by: 52
Author(s): Tatu Pantsar, Sami Rissanen, Daniel Dauch, Tuomo Laitinen, Ilpo Vattulainen, Antti Poso
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1007714

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex
Cited by: 11
Author(s): Dmitrii S. Shcherbinin, Vlad A. Belousov, Mikhail Shugay
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1003749

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
Cited by: 27
Author(s): Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Élodie Laine, Alain Trouvé, Patrice Dubreuil, Luba Tchertanov
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1002674

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
Cited by: 28
Author(s): Andrei V. Pisliakov, Tsuneo Hino, Yoshitsugu Shiro, Yuji Sugita
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1000367

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)
Cited by: 26
Author(s): Srinivas Ramachandran, Adrian W.R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1002929

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
Cited by: 46
Author(s): Pouria Dasmeh, Adrian W.R. Serohijos, Kasper Planeta Kepp, Eugene I. Shakhnovich
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1004282

Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2
Cited by: 20
Author(s): Juan A. Bueren-Calabuig, Julien Michel
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1004556

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
Cited by: 132
Author(s): David Bednář, Koen Beerens, Eva Šebestová, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupková, Zbyněk Prokop, Jan Brezovský, David Baker, Jiřı́ Damborský
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.1005948

The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
Cited by: 17
Author(s): Ravi Kumar Verma, Ara M. Abramyan, Mayako Michino, R. Benjamin Free, David R. Sibley, Jonathan A. Javitch, J. Robert Lane, Lei Shi
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1000772

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences
Cited by: 92
Author(s): Vinal Lakhani, Feng Ding, Nikolay V. Dokholyan
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1004834

Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
Cited by: 18
Author(s): Sandhya Tiwari, Nathalie Reuter
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1001042

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation
Cited by: 20
Author(s): Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1007881

Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis
Cited by: 25
Author(s): Jia-Chi Ku, Arnaud Ronceret, Inna N. Golubovskaya, Ding Hua Lee, Rachel Wang, Ljudmilla Timofejeva, Yu-Hsin Kao, Ana Karen Gomez Angoa, Karl A. Kremling, Rosalind Williams‐Carrier, Robert B. Meeley, Alice Barkan, W. Zacheus Cande
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1008208

Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies
Cited by: 24
Author(s): Sook Wah Yee, Adrian Stecula, Huan‐Chieh Chien, Ling Zou, Elena V. Feofanova, Marjolein van Borselen, Kit Wun Kathy Cheung, Noha A. Yousri, Karsten Suhre, Jason M. Kinchen, Eric Boerwinkle, Roshanak Irannejad, Bing Yu, Kathleen M. Giacomini
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1004784

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response
Cited by: 122
Author(s): Erin Becker, Phillip Seitzer, Andrew Tritt, David Larsen, Megan L. Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling, Marc T. Facciotti
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007009

Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model
Cited by: 21
Author(s): Edward B. Li, Dawn Truong, Shawn A Hallett, Kusumika Mukherjee, Brian C. Schutte, Eric C. Liao
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1008224

The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals
Cited by: 30
Author(s): Amy E. Rohlfing, B.E. Eckenroth, Emily R. Forster, Yuzo Kevorkian, M. Lauren Donnelly, Hector Benito de la Puebla, Sylvie Doublié, Aimee Shen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006897

Altered paracellular cation permeability due to a rare CLDN10B variant causes anhidrosis and kidney damage
Cited by: 48
Author(s): Joakim Klar, Jörg Piontek, Susanne Milatz, Muhammad Tariq, Muhammad Jameel, Tilman Breiderhoff, Jens Schuster, Ambrin Fatima, Maria Asif, Muhammad Sher, Katrin Mäbert, Anja Fromm, Shahid Mahmood Baig, Dorothee Günzel, Niklas Dahl
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006844

Differential regulation of polarized synaptic vesicle trafficking and synapse stability in neural circuit rewiring in Caenorhabditis elegans
Cited by: 8
Author(s): N S Kurup, Dong Yan, Karina Kono, Yishi Jin
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1000688

A Novel System of Polymorphic and Diverse NK Cell Receptors in Primates
Cited by: 65
Author(s): Anne Averdam, Beatrix Petersen, Cornelia Rosner, Jennifer Neff, Christian Roos, M. Eberle, Fabienne Aujard, Claudia Münch, Werner Schempp, Mary Carrington, Takashi Shiina, Hidetoshi Inoko, Florian Knaust, Penny Coggill, Harminder Sehra, Stephan Beck, Laurent Abi-Rached, Richard Reinhardt, Lutz Walter
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1007853

In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation
Cited by: 26
Author(s): Nick Brouwers, Arthur R. Gorter de Vries, Marcel van den Broek, Susan M Weening, Tom D. Elink Schuurman, Niels G. A. Kuijpers, Jack T. Pronk, Jean‐Marc Daran
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1005434

Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii
Cited by: 79
Author(s): Michael S. Behnke, Asis Khan, Elvin J. Lauron, John R. Jimah, Qiuling Wang, Niraj H. Tolia, L. David Sibley
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1002783

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme
Cited by: 82
Author(s): Martijn Schenk, Ivan G. Szendro, Joachim Krug, Jaap Visser
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1005228

Mutations in RECQL Gene Are Associated with Predisposition to Breast Cancer
Cited by: 84
Author(s): Jie Sun, Yuxia Wang, Yisui Xia, Ye Xu, Tao Ouyang, Jinfeng Li, Tianfeng Wang, Zhaoqing Fan, Tie Fan, Benyao Lin, Huiqiang Lou, Yuntao Xie
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006376

Secretion-Positive LGI1 Mutations Linked to Lateral Temporal Epilepsy Impair Binding to ADAM22 and ADAM23 Receptors
Cited by: 19
Author(s): Emanuela Dazzo, Emanuela Leonardi, Elisa Belluzzi, Sandro Malacrida, Libero Vitiello, Elisa Greggio, Silvio C. E. Tosatto, Carlo Nobile
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1005618

Allelic Variation of Cytochrome P450s Drives Resistance to Bednet Insecticides in a Major Malaria Vector
Cited by: 73
Author(s): Sulaiman S. Ibrahim, Jacob M. Riveron, Jaclyn Bibby, Helen Irving, Cristina Yunta, Mark J. I. Paine, Charles S. Wondji
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1005469

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)
Cited by: 54
Author(s): Blake T. Hovde, Chloe R. Deodato, Heather M. Hunsperger, Scott A. Ryken, Will Yost, Ramesh K. Jha, Johnathan Patterson, Raymond J. Monnat, Steven B. Barlow, Shawn R. Starkenburg, Rose Ann Cattolico
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1002965

Phosphatase-Dead Myotubularin Ameliorates X-Linked Centronuclear Myopathy Phenotypes in Mice
Cited by: 49
Author(s): Leonela Amoasii, Dimitri L. Bertazzi, Hélène Tronchère, Karim Hnia, Gaëtan Chicanne, Bruno Rinaldi, Belinda S. Cowling, Arnaud Ferry, Bruno P. Klaholz, Bernard Payrastre, Jocelyn Laporte, Sylvie Friant
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1007671

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay
Cited by: 16
Author(s): Susan M. Hiatt, Matthew B. Neu, Ryne C. Ramaker, Andrew A. Hardigan, Jeremy W. Prokop, Miroslava Hančárová, Darina Prchalová, Markéta Havlovičová, Jan Prchal, Viktor Stránecký, Dwight K.C Yim, Zöe Powis, Boris Keren, Caroline Nava, Cyril Mignot, Marlène Rio, Anya Revah‐Politi, Parisa Hemati, Nicholas Stong, Alejandro Iglesias, Sharon F. Suchy, Rebecca Willaert, Ingrid M. Wentzensen, Patricia G. Wheeler, Lauren Brick, Mariya Kozenko, Anna Hurst, James W. Wheless, Yves Lacassie, R Myers, Gregory S. Barsh, Zdeněk Sedláček, Gregory M. Cooper
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1006974

mlh3 mutations in baker’s yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide
Cited by: 30
Author(s): Najla Al‐Sweel, Vandana Raghavan, Abhishek Dutta, V. P. Ajith, Luigi Di Vietro, Nabila Khondakar, Carol M. Manhart, Jennifer A. Surtees, K. T. Nishant, Eric Alani
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1008400

Evolution of the Auxin Response Factors from charophyte ancestors
Cited by: 33
Author(s): Raquel Martín-Arevalillo, Emmanuel Thévenon, Fanny Jégu, Thomas Vinos-Poyo, Teva Vernoux, François Parcy, Renaud Dumas
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1005745

Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities
Cited by: 21
Author(s): Xiaoyun Wang, Tao Pan
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1005540

Cell-Autonomous Gβ Signaling Defines Neuron-Specific Steady State Serotonin Synthesis in Caenorhabditis elegans
Cited by: 6
Author(s): Lu Xu, Sunju Choi, Yusu Xie, Ji Ying Sze
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1006214

Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection
Cited by: 19
Author(s): Nils Poulicard, Luis F. Pacios, Jean‐Luc Gallois, Daniel Piñero, Fernando García-Arénal
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1000301

Compensatory Interactions between Sir3p and the Nucleosomal LRS Surface Imply Their Direct Interaction
Cited by: 42
Author(s): Anne Norris, M.A. Bianchet, Jef D. Boeke
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pgen.1005941

Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics
Cited by: 22
Author(s): Bartholomew P. Roland, Alison M. Zeccola, Samantha B. Larsen, Christopher G. Amrich, Aaron D Talsma, Kimberly A. Stuchul, A. Héroux, Edwin S. Levitan, Andrew P. VanDemark, Michael J. Palladino
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0036635

Crystal Structure of the Cysteine Desulfurase DndA from Streptomyces lividans Which Is Involved in DNA Phosphorothioation
Cited by: 16
Author(s): Fukun Chen, Zhenyi Zhang, Kui Lin, Tianle Qian, Yan Zhang, Delin You, Xinyi He, Zhijun Wang, Liang Ji, Zixin Deng, Geng Wu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0070336

Structural Integrity of the Greek Key Motif in βγ-Crystallins Is Vital for Central Eye Lens Transparency
Cited by: 42
Author(s): Venkata Pulla Rao Vendra, Garima Agarwal, Sushil Chandani, Venu Talla, Narayanaswamy Srinivasan, D. Balasubramanian
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0126970

Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin
Cited by: 9
Author(s): Midori Murakami, Tsutomu Kouyama
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0220918

Structural and functional analysis of the Acinetobacter baumannii BlsA photoreceptor and regulatory protein
Cited by: 7
Author(s): Cecily R. Wood, Mariah S. Squire, Natosha L. Finley, Richard C. Page, Luis A. Actis
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0074477

Protein Similarity Networks Reveal Relationships among Sequence, Structure, and Function within the Cupin Superfamily
Cited by: 55
Author(s): Richard Uberto, Ellen W. Moomaw
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0018791

Identification of Amino Acids that Account for Long-Range Interactions in Two Triosephosphate Isomerases from Pathogenic Trypanosomes
Cited by: 15
Author(s): Itzhel García-Torres, Nallely Cabrera, Alfredo Torres‐Larios, Mónica Rodríguez-Bolaños, Selma Díaz-Mazariegos, Armando Gómez‐Puyou, Ruy Pérez‐Montfort
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0051179

Enhancing E. coli Tolerance towards Oxidative Stress via Engineering Its Global Regulator cAMP Receptor Protein (CRP)
Cited by: 50
Author(s): Souvik Basak, Rongrong Jiang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0054568

Towards Tricking a Pathogen’s Protease into Fighting Infection: The 3D Structure of a Stable Circularly Permuted Onconase Variant Cleavedby HIV-1 Protease
Cited by: 6
Author(s): Mariona Callís, Susana Serrano, Antoni Benito, Douglas V. Laurents, María Vilanova, Marta Bruix, Marc Ribó
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0239350

RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that might result in limited and differential promoter recognition
Cited by: 3
Author(s): Cynthia Paola Rangel-Chávez, Edgardo Galán-Vásquez, Azucena Pescador-Tapia, Luis Delaye, Agustino Martı́nez-Antonio
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0200014

PIK3CA missense mutations promote glioblastoma pathogenesis, but do not enhance targeted PI3K inhibition
Cited by: 18
Author(s): Robert S. McNeill, Emily E. Stroobant, Erin Smithberger, Demitra A. Canoutas, Madison Butler, Abigail Shelton, Shrey Patel, Juanita C. Limas, Kasey R Skinner, Ryan Bash, Ralf S. Schmid, C. Ryan Miller
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0211525

Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in Trypanosome holo-editosomes
Cited by: 4
Author(s): Vijoy Kumar, Pawan Kumar Doharey, Shelly Gulati, Joshua Meehan, Mary Grace Martinez, Karrisa Hughes, Blaine H. M. Mooers, Jorge Cruz‐Reyes
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0050660

Molecular Evolution of Hemagglutinin (H) Gene in Measles Virus Genotypes D3, D5, D9, and H1
Cited by: 12
Author(s): Masaaki Saitoh, Makoto Takeda, Koichi Gotoh, Fumihiko Takeuchi, Tsuyoshi Sekizuka, Makoto Kuroda, Katsumi Mizuta, Akihide Ryo, Ryota Tanaka, Haruyuki Ishii, Hayato Takada, Kunihisa Kozawa, Ayako Yoshida, Masahiro Noda, Nobuhiko Okabe, Hirokazu Kimura
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0019670

An Algebro-Topological Description of Protein Domain Structure
Cited by: 14
Author(s): Robert Penner, Michael Knudsen, Carsten Wiuf, Jørgen Ellegaard Andersen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0096627

Sets of Covariant Residues Modulate the Activity and Thermal Stability of GH1 β-Glucosidases
Cited by: 11
Author(s): Fábio K. Tamaki, Larissa C. Textor, Igor Polikarpov, Sandro R. Marana
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0117798

Analysis of Structural Flexibility of Damaged DNA Using Thiol-Tethered Oligonucleotide Duplexes
Cited by: 2
Author(s): Masashi Fujita, Satoshi Watanabe, Mariko Yoshizawa, Junpei Yamamoto, Shigenori Iwai
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0183500

The stability of Fbw7α in M-phase requires its phosphorylation by PKC
Cited by: 4
Author(s): Sihem Zitouni, Francisca Méchali, Catherine Papin, Armelle Choquet, Daniel B. Roche, Véronique Baldin, Olivier Coux, Catherine Bonne-Andréa
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0184278

A fully humanized IgG-like bispecific antibody for effective dual targeting of CXCR3 and CCR6
Cited by: 20
Author(s): Rémy Robert, Laurent Juglair, Ee X. Lim, Caroline Ang, Carl J. H. Wang, Gregor Ebert, Olan Dolezal, Charles R. Mackay
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0019923

Hydrogen Bonding Penalty upon Ligand Binding
Cited by: 74
Author(s): Hongtao Zhao, Danzhi Huang
Software Mentions: 1
Published: over 13 years ago

Projects: pypi: PyMOL

Papers Mentioning PyMOL 8,266