10.1111/cns.13627

High‐sensitive clinical diagnostic method for PTPRZ1‐MET and the characteristic protein structure contributing to ligand‐independent MET activation
Cited by: 5
Author(s): Ruoyu Huang, Yanwei Liu, Kuanyu Wang, Zheng Wang, Chuanbao Zhang, Wei Zhang, Zheng Zhao, Guanzhang Li, Lijie Huang, Yuanhao Chang, Fan Zeng, Tao Jiang, Huimin Hu
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.25149

Disturbed alternative splicing of FIR (PUF60) directed cyclin E overexpression in esophageal cancers
Cited by: 8
Author(s): Yukiko Ogura, Tyuji Hoshino, Nobuko Tanaka, Guzhanuer Ailiken, Sohei Kobayashi, Kazuo Kïtamura, Bahityar Rahmutulla, Masayuki Kano, Kentarou Murakami, Yasunori Akutsu, Fumio Nomura, Sakae Itoga, Hisahiro Matsubara, Hiroshi Matsushita
Software Mentions: 1
Published: about 8 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: about 8 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: over 18 years ago

10.1186/s12896-015-0217-x

Defining the complementarities between antibodies and haptens to refine our understanding and aid the prediction of a successful binding interaction
Cited by: 13
Author(s): Mohammed M. Al Qaraghuli, Soumya Palliyil, Gillian Broadbent, David C. Cullen, Keith A. Charlton, A.J. Porter
Software Mentions: 1
Published: over 10 years ago

10.1016/j.str.2017.04.013

Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1
Cited by: 42
Author(s): Katja K. Dove, Jennifer L. Olszewski, Luigi Martino, David M. Duda, Xiaoli Wu, Darcie J. Miller, Katherine H. Reiter, Katrin Rittinger, Brenda A. Schulman, Rachel E. Klevit
Software Mentions: 1
Published: about 9 years ago

10.1016/j.str.2017.05.005

Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARA/Endofin with HD-PTP
Cited by: 12
Author(s): Deepankar Gahloth, Colin Levy, Larry P. Walker, Lydia Wunderley, A. Paul Mould, Sandra Taylor, Philip Woodman, Lydia Tabernero
Software Mentions: 1
Published: about 9 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 18 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: over 11 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: over 8 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: over 5 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: over 13 years ago

10.1186/s42269-020-00479-6

Luteolin and abyssinone II as potential inhibitors of SARS-CoV-2: an in silico molecular modeling approach in battling the COVID-19 outbreak
Cited by: 49
Author(s): Mohammad Mahfuz Ali Khan Shawan, Sajal Kumar Halder, Md. Ashraful Hasan
Software Mentions: 1
Published: over 5 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: over 18 years ago

10.3390/ijms18071408

Identification of Direct Activator of Adenosine Monophosphate-Activated Protein Kinase (AMPK) by Structure-Based Virtual Screening and Molecular Docking Approach
Cited by: 13
Author(s): Tonghui Huang, Jie Sun, Shenghan Zhou, Jian Gao, Yi Liu
Software Mentions: 1
Published: about 9 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: almost 20 years ago

10.1016/j.str.2017.10.004

The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
Cited by: 43
Author(s): Manuela K. Hospenthal, Dawid Zyla, Tiago Costa, Adam Redzej, Christoph Giese, James Lillington, Rudi Glockshuber, Gabriel Waksman
Software Mentions: 1
Published: over 8 years ago

10.1016/j.str.2017.11.008

Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes
Cited by: 31
Author(s): Vito Genna, Matteo Colombo, Marco De Vivo, Marco Marcia
Software Mentions: 1
Published: over 8 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 14 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: over 16 years ago

10.1093/bib/bbab056

A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium
Cited by: 15
Author(s): Jim Warwicker
Software Mentions: 1
Published: over 5 years ago

10.1093/bib/bbt043

Best practices in bioinformatics training for life scientists
Cited by: 50
Author(s): Allegra Via, Thomas Blicher, Erik Bongcam‐Rudloff, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Pedro Fernandes, Celia van Gelder, Joachim Jacob, Rafael C. Jiménez, Jane Loveland, Federico Morán, Nicola Mulder, Tommi Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood
Software Mentions: 1
Published: about 13 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: about 17 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: over 5 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: almost 8 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 6 years ago

10.1016/j.str.2017.12.003

Robo1 Forms a Compact Dimer-of-Dimers Assembly
Cited by: 24
Author(s): Наталія Александрова, Irina Gutsche, Eaazhisai Kandiah, Sergiy V. Avilov, Maxim V. Petoukhov, E. Seiradake, A.A. McCarthy
Software Mentions: 1
Published: over 8 years ago

10.1186/1472-6750-13-71

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiaeidentifies mutants with improved heterologous exocellulase activity and host secretion
Cited by: 31
Author(s): Tzi‐Yuan Wang, Chih-Jen Huang, Hsin‐Liang Chen, Po-Chun Ho, Huei-Mien Ke, Hsing-Yi Cho, Sz-Kai Ruan, Kuo-Yen Hung, I-Li Wang, Ya-Wun Cai, Huang‐Mo Sung, Wen-Hsiung Li, Ming-Che Shih
Software Mentions: 1
Published: almost 13 years ago

10.1016/j.str.2018.02.007

Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB
Cited by: 12
Author(s): Santiago Martínez-Lumbreras, Caterina Alfano, N.J. Evans, Katherine M. Collins, Kelly A. Flanagan, R. Andrew Atkinson, E. Krysztofinska, Anupama Vydyanath, Jacquelin Jackter, Sarah Fixon-Owoo, Amy H. Camp, Rivka L. Isaacson
Software Mentions: 1
Published: over 8 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: almost 12 years ago

10.1016/j.str.2018.03.019

The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors
Cited by: 29
Author(s): Daniel L. Hurdiss, Martin Frank, Joseph S. Snowden, Andrew Macdonald, Neil A. Ranson
Software Mentions: 1
Published: about 8 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: almost 14 years ago

10.3390/ijms18071535

Recombinant Lipase from Gibberella zeae Exhibits Broad Substrate Specificity: A Comparative Study on Emulsified and Monomolecular Substrate
Cited by: 12
Author(s): Fanghua Wang, Hui Zhang, Zhongyang Zhao, Ruixia Wei, Bo Yang, Yonghua Wang
Software Mentions: 1
Published: about 9 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: about 17 years ago

10.1155/2021/6471400

Molecular Mechanism of Jinchan Oral Liquid in the Treatment of Children with Respiratory Syncytial Virus Pneumonia Based on Network Pharmacology and Molecular Docking Technology
Cited by: 3
Author(s): Li Shen, Yiguo Jiang, Jin Lu, Guangfei Wang, Xiaolan Zhang, Shiwen He, Cheng Wang, Zhiping Li
Software Mentions: 1
Published: almost 5 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 13 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: about 11 years ago

10.3390/ijms18081680

Various Mechanisms Involve the Nuclear Factor (Erythroid-Derived 2)-Like (NRF2) to Achieve Cytoprotection in Long-Term Cisplatin-Treated Urothelial Carcinoma Cell Lines
Cited by: 13
Author(s): Margaretha A. Skowron, Günter Niegisch, Philipp Albrecht, Gommert van Koeveringe, Andrea Romano, Peter Albers, Wolfgang A. Schulz, Michèle J. Hoffmann
Software Mentions: 1
Published: almost 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: over 10 years ago

10.1155/2014/971345

Novel Bifunctional Single-Chain Variable Antibody Fragments to Enhance Virolysis by Complement: Generation and Proof-of-Concept
Cited by: 2
Author(s): G. Carl Huber, Zoltán Bánki, Renate Kunert, Heribert Stoiber
Software Mentions: 1
Published: over 12 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: over 8 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: about 16 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 10 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: over 15 years ago

10.1155/2015/402536

Predicting Flavin and Nicotinamide Adenine Dinucleotide-Binding Sites in Proteins Using the Fragment Transformation Method
Cited by: 3
Author(s): Chih-Hao Lu, Chao Yu, Yu‐Feng Lin, Jinyi Chen
Software Mentions: 1
Published: over 11 years ago

10.1155/2014/389869

Carborane-Based Carbonic Anhydrase Inhibitors: Insight into CAII/CAIX Specificity from a High-Resolution Crystal Structure, Modeling, and Quantum Chemical Calculations
Cited by: 17
Author(s): P. Mäder, Adam Pecina, Petr Cígler, Martin Lepšı́k, Václav Šícha, Pavel Hobza, Bohumı́r Grüner, Jindřich Fanfrlík, J. Brynda, P. Řezáčová
Software Mentions: 1
Published: over 12 years ago

10.1016/j.str.2018.12.001

Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit
Cited by: 16
Author(s): Valérie Campanacci, Agathe Urvoas, Tanja Consolati, Soraya Cantos-Fernandes, Magali Aumont-Niçaise, Marie Valerio-Lepiniec, Thomas Surrey, Philippe Minard, B. Gigant
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms18091848

Tongue Sole CD209: A Pattern-Recognition Receptor that Binds a Broad Range of Microbes and Promotes Phagocytosis
Cited by: 16
Author(s): Shuai Jiang, Li Sun
Software Mentions: 1
Published: almost 9 years ago

10.1155/2014/342725

Crystal Structure of<i>Deinococcus radiodurans</i>RecQ Helicase Catalytic Core Domain: The Interdomain Flexibility
Cited by: 5
Author(s): Sheng-Chia Chen, Chi‐Hung Huang, Changju Yang, Tzong‐Der Way, Mau Song Chang, Yeh Chen
Software Mentions: 1
Published: over 12 years ago

10.1155/2018/9538193

Biochemical and Biophysical Characterization of the Enolase from<i>Helicobacter pylori</i>
Cited by: 8
Author(s): María de Jesús López-López, Isabel Cristina Rodríguez-Luna, Edgar E. Lara-Ramírez, Marisol López-Hidalgo, Claudia G. Benítez‐Cardoza, Xianwu Guo
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms18091894

Differences in Sulfotyrosine Binding amongst CXCR1 and CXCR2 Chemokine Ligands
Cited by: 11
Author(s): Natasha A. Moussouras, Anthony E. Getschman, Emily R. Lackner, Christopher T. Veldkamp, Michael B. Dwinell, Brian F. Volkman
Software Mentions: 1
Published: almost 9 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: about 6 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: almost 7 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: over 11 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: almost 9 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: about 7 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: about 9 years ago

10.1155/2014/291214

Dual Binding Site and Selective Acetylcholinesterase Inhibitors Derived from Integrated Pharmacophore Models and Sequential Virtual Screening
Cited by: 31
Author(s): Shikhar Gupta, C. Gopi Mohan
Software Mentions: 1
Published: over 12 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: about 9 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: almost 17 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 7 years ago

10.3390/ijms18091898

Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation
Cited by: 6
Author(s): Hongliang Liu, Qing Wei, Chenyang Huang, Yong Zhang, Zekun Guo
Software Mentions: 1
Published: almost 9 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: almost 11 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: about 14 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: about 11 years ago

10.3390/ijms18091968

Tumor Inhibitory Effect of IRCR201, a Novel Cross-Reactive c-Met Antibody Targeting the PSI Domain
Cited by: 9
Author(s): Hyunkyu Park, Donggeon Kim, Eun‐Mi Kim, K. Jason, Hee Won Lee, Suji Yu, Joosung Oh, Seok Hyung Kim, Yong‐Ho Yoon, Do Hyun Nam
Software Mentions: 1
Published: almost 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: over 9 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: over 10 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: almost 11 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: almost 14 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: over 7 years ago

10.3390/ijms18112398

Identification, Expression, and Functional Analysis of the Fructokinase Gene Family in Cassava
Cited by: 17
Author(s): Yuan Yao, Meiyu Geng, Xiaohui Wu, Chong Sun, Yunlin Wang, Xia Chen, Lei Shang, Xiaohua Lü, Li Zhan, Ruimei Li, Shaoping Fu, Ran Duan, Jiao Liu, Xinwen Hu, Jiao Guo
Software Mentions: 1
Published: over 8 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: almost 9 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: almost 7 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: over 10 years ago

10.1186/2046-1682-5-2

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations
Cited by: 23
Author(s): Haina Qin, Liangzhong Lim, Jianxing Song
Software Mentions: 1
Published: over 14 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: almost 11 years ago

10.1155/2013/851428

Extremophilic SHMTs: From Structure to Biotechnology
Cited by: 19
Author(s): Sebastiana Angelaccio
Software Mentions: 1
Published: over 13 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: almost 10 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: over 17 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 10 years ago

10.3390/ijms18122623

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures
Cited by: 14
Author(s): John Oliver Nealon, Limcy Seby Philomina, Liam J. McGuffin
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0141718

Natural Guided Genome Engineering Reveals Transcriptional Regulators Controlling Quorum-Sensing Signal Degradation
Cited by: 6
Author(s): Abbas El Sahili, Anthony Kwasiborski, Nicolas Mothe, Christophe Velours, Pierre Legrand, S. Morera, Denis Faure
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0144506

Hypoxia-Targeted Drug Q6 Induces G2-M Arrest and Apoptosis via Poisoning Topoisomerase II under Hypoxia
Cited by: 9
Author(s): Ling‐Sai Chang, Xiaowen Liu, Dandan Wang, Jian Ma, Tianyi Zhou, Ying Chen, Rong Sheng, Yongzhou Hu, Ying Du, Qiaojun He, Bo Yang, Hong Zhu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0063870

Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA
Cited by: 15
Author(s): Dazhi Tan, Warren M. Crabb, William B. Whitman, Liang Tong
Software Mentions: 1
Published: about 13 years ago

10.1016/j.str.2020.05.010

Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase
Cited by: 12
Author(s): Samual D. Dick, Stefania Federico, Simon Hughes, V.E. Pye, Nicola O’Reilly, Peter Cherepanov
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0053347

G-Protein Coupled Receptor 83 (GPR83) Signaling Determined by Constitutive and Zinc(II)-Induced Activity
Cited by: 28
Author(s): Anne Müller, Gunnar Kleinau, Carolin Leonie Piechowski, Timo Müller, Brian Finan, Juliane Pratzka, Annette Grüters, Heiko Krude, Matthias H. Tschöp, Heike Biebermann
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0026245

Elucidation of the ATP7B N-Domain Mg2+-ATP Coordination Site and Its Allosteric Regulation
Cited by: 2
Author(s): Claude Hercend, Cyril Bauvais, Guillaume Bollot, Nicolas Delacotte, P. Chappuis, F. Woimant, Jean‐Marie Launay, Philippe Manivet
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0161909

In Silico and Biochemical Characterization of Lysozyme-Like Proteins in the Rat
Cited by: 13
Author(s): Ganapathy Narmadha, Suresh Yenugu
Software Mentions: 1
Published: almost 10 years ago

10.1186/1475-925X-8-14

Book review of Structural Bioinformatics: An Algorithmic Approach by Forbes J. Burkowski
Cited by: 0
Author(s): Ilza Pajeva
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0153373

The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG
Cited by: 4
Author(s): François P. Douillard, Pia Rasinkangas, Arnab Bhattacharjee, Airi Palva, Willem M. de Vos
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0102040

A Unique Mono- and Diacylglycerol Lipase from Penicillium cyclopium: Heterologous Expression, Biochemical Characterization and Molecular Basis for Its Substrate Selectivity
Cited by: 12
Author(s): Zhiyong Tan, Jianfang Li, Xueting Li, Yunfu Gu, Minchen Wu, Jang‐Yen Wu, Junqing Wang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0162926

The Effectiveness of Natural Diarylheptanoids against Trypanosoma cruzi: Cytotoxicity, Ultrastructural Alterations and Molecular Modeling Studies
Cited by: 18
Author(s): Vitor Sueth-Santiago, Julliane de Brito Braz Moraes, Eliomara Sousa Sobral Alves, Marcos A. Vannier-Santos, Célio Geraldo Freire-de-Lima, Rosane Nora Castro, Gustavo Peron Mendes-Silva, Catarina de Nigris Del Cistia, Luma G. Magalhães, Adriano D. Andricopulo, Carlos Maurício R. Sant ́Anna, Débora Decotè-Ricardo, Marco Edílson Freire de Lima
Software Mentions: 1
Published: almost 10 years ago

10.1186/s40364-021-00286-9

Pathophysiological roles of myristoylated alanine-rich C-kinase substrate (MARCKS) in hematological malignancies
Cited by: 7
Author(s): Deepak Narayanan Iyer, Omar Faruq, Lun Zhang, Nasrin Rastgoo, Aijun Liu, Hong Chang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0104242

Computational Screening and Molecular Dynamic Simulation of Breast Cancer Associated Deleterious Non-Synonymous Single Nucleotide Polymorphisms in TP53 Gene
Cited by: 36
Author(s): Kumaraswamy Naidu Chitrala, Y. Suneetha
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0117724

The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation
Cited by: 8
Author(s): Kevin M. Dalton, Judith Frydman, Vijay S. Pande
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0097051

Inter-Species Cross-Seeding: Stability and Assembly of Rat - Human Amylin Aggregates
Cited by: 27
Author(s): Workalemahu M. Berhanu, Ulrich H. E. Hansmann
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0117508

Anti-HmuY Antibodies Specifically Recognize Porphyromonas gingivalis HmuY Protein but Not Homologous Proteins in Other Periodontopathogens
Cited by: 17
Author(s): Michał Śmiga, Marcin Bielecki, Mariusz Olczak, John W. Smalley, Teresa Olczak
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0147485

Exploring the Mechanism Responsible for Cellulase Thermostability by Structure-Guided Recombination
Cited by: 30
Author(s): Chia‐Jung Chang, Cheng-Chung Lee, Yueh-Te Chan, Devin L. Trudeau, Mingqiu Wu, Chih-Hsuan Tsai, Su‐May Yu, Tuan‐Hua David Ho, Andrew H.-J. Wang, Chwan‐Deng Hsiao, Frances H. Arnold, Yu-Chan Chao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0147596

Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants
Cited by: 40
Author(s): Dylan Alexander Carlin, Ryan Caster, Xiaokang Wang, Stephanie A. Betzenderfer, Claire X. Chen, Veasna M. Duong, Carolina V. Ryklansky, Alp Alpekin, Nathan Beaumont, Harshul Kapoor, Nicole Kim, Hosna Mohabbot, Boyu Pang, Rachel Teel, Lillian Whithaus, Ilias Tagkopoulos, Justin B. Siegel
Software Mentions: 1
Published: over 10 years ago