10.1371/journal.pgen.1005720

Co-evolution of Bacterial Ribosomal Protein S15 with Diverse mRNA Regulatory Structures
Cited by: 14
Author(s): Betty L. Slinger, Hunter Newman, Young Han Lee, Shermin Pei, Michelle M. Meyer
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pmed.0030485

Epidermal Growth Factor Receptor Activation in Glioblastoma through Novel Missense Mutations in the Extracellular Domain
Cited by: 306
Author(s): Jeffrey C. Lee, Igor Vivanco, Rameen Beroukhim, Julie H. Huang, Whei Feng, Ralph DeBiasi, Koji Yoshimoto, Jennifer C. King, Phioanh L. Nghiemphu, Yuki Yuza, Qingqing Xu, Heidi Greulich, Roman K. Thomas, J. Guillermo Páez, Timothy C. Peck, David Linhart, Karen A. Glatt, Gad Getz, Robert C. Onofrio, Liuda Ziaugra, Ross L. Levine, Stacey Gabriel, Tomohiro Kawaguchi, Keith O'Neill, Haumith Khan, Linda M. Liau, Stanley F. Nelson, P. Nagesh Rao, Paul S. Mischel, Russell O. Pieper, Timothy F. Cloughesy, Daniel J. Leahy, William R. Sellers, Charles L. Sawyers, Matthew Meyerson, Ingo K. Mellinghoff
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pntd.0004365

Leishmania infantum Asparagine Synthetase A Is Dispensable for Parasites Survival and Infectivity
Cited by: 8
Author(s): Joana Faria, Inês Loureiro, Nuno Santarém, Sandra Macedo-Ribeiro, Joana Tavares, Anabela Cordeiro-da-Silva
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pntd.0003430

Ribose 5-Phosphate Isomerase B Knockdown Compromises Trypanosoma brucei Bloodstream Form Infectivity
Cited by: 18
Author(s): Inês Loureiro, Joana Faria, Christine Clayton, Sandra Macedo-Ribeiro, Nuno Santarém, Nilanjan Roy, Anabela Cordeiro-da-Siva, Joana Tavares
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pntd.0001559

Biochemical, Mutational and In Silico Structural Evidence for a Functional Dimeric Form of the Ornithine Decarboxylase from Entamoeba histolytica
Cited by: 8
Author(s): . Preeti, Satya Tapas, Pravindra Kumar, Rentala Madhubala, Shailly Tomar
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pntd.0006969

Identification and binding mode of a novel Leishmania Trypanothione reductase inhibitor from high throughput screening
Cited by: 40
Author(s): Lorenzo Turcano, Esther Torrente, Antonino Missineo, Matteo Andreini, Marina Gramiccia, Trentina Di Muccio, Ilaria Genovese, Annarita Fiorillo, Steven J. Harper, Alberto Bresciani, Gianni Colotti, Andrea Ilari
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0002492

Exploring the Trypanosoma brucei Hsp83 Potential as a Target for Structure Guided Drug Design
Cited by: 36
Author(s): J.C. Pizarro, T. Hills, Guillermo Senisterra, A.K. Wernimont, Claire J. Mackenzie, Neil R. Norcross, Michael A. J. Ferguson, Paul G. Wyatt, Ian H. Gilbert, Raymond Hui
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0008517

An iterative process produces oxamniquine derivatives that kill the major species of schistosomes infecting humans
Cited by: 10
Author(s): Meghan A. Guzman, Anastasia R. Rugel, Reid S. Tarpley, Sevan N. Alwan, Frédéric D. Chevalier, Dmytro Kovalskyy, Xiaoguang Cao, S. Holloway, Timothy J. Anderson, Alexander B. Taylor, Stanton F. McHardy, Philip T. LoVerde
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pntd.0002947

Simplagrin, a Platelet Aggregation Inhibitor from Simulium nigrimanum Salivary Glands Specifically Binds to the Von Willebrand Factor Receptor in Collagen and Inhibits Carotid Thrombus Formation In Vivo
Cited by: 12
Author(s): Andrezza Campos Chagas, Peter McPhie, Hong San, David L. Narum, Karine Reiter, Fuyuki Tokomasu, Fábio André Brayner, Luíz Carlos Alves, José M. C. Ribeiro, Eric Calvo
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pntd.0005217

In vivo Distribution and Clearance of Purified Capsular Polysaccharide from Burkholderia pseudomallei in a Murine Model
Cited by: 12
Author(s): Teerapat Nualnoi, Adam Kirosingh, Sujata G. Pandit, Peter Thorkildson, Paul J. Brett, Mary N. Burtnick, David P. AuCoin
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0002482

On the Three-Finger Protein Domain Fold and CD59-Like Proteins in Schistosoma mansoni
Cited by: 26
Author(s): Leonardo P. Farias, Greice Krautz‐Peterson, Cibele Aparecida Tararam, Bogar O. Araujo-Montoya, Tatiana R. Fraga, Henrique K. Rofatto, Floriano Paes Silva, Lourdes Isaac, Akram A. Da’dara, R. A. Wilson, Charles B. Shoemaker, Luciana C. C. Leite
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0000356

Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking
Cited by: 70
Author(s): Dariusz Ekonomiuk, Xun‐Cheng Su, Kiyoshi Ozawa, Christophe Bodenreider, Siew Pheng Lim, Zheng Yin, Thomas H. Keller, David Beer, Viral Patel, Gottfried Otting, Amedeo Caflisch, Danzhi Huang
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pntd.0003903

An Epitope-Substituted DNA Vaccine Improves Safety and Immunogenicity against Dengue Virus Type 2
Cited by: 18
Author(s): Chung-Tao Tang, Pi-Chun Li, I-Ju Liu, Minfu Liao, Chiung-Yi Chiu, Day‐Yu Chao, Han‐Chung Wu
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0003920

Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment
Cited by: 17
Author(s): Iain W. Chalmers, Colin M. Fitzsimmons, Martha Brown, Christine Pierrot, Frances M. Jones, Jakub Wawrzyniak, Narcís Fernández-Fuentes, Edridah M. Tukahebwa, David W. Dunne, Jamal Khalife, Karl F. Hoffmann
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0007915

Identification and validation of specific B-cell epitopes of hantaviruses associated to hemorrhagic fever and renal syndrome
Cited by: 12
Author(s): Fernando de Paiva Conte, Bianca Corrêa Tinoco, Thiago Santos Chaves, Renata Carvalho de Oliveira, Janaina Figueira Mansur, Ronaldo Mohana‐Borges, Elba Regina Sampaio de Lemos, Patrícia Cristina da Costa Neves, Rodrigo Nunes Rodrigues-da-Silva
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0005720

Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions
Cited by: 4
Author(s): Leah M. Wachsmuth, Meredith G. Johnson, Jason Gavenonis
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pntd.0008458

Instability of aquaglyceroporin (AQP) 2 contributes to drug resistance in Trypanosoma brucei
Cited by: 9
Author(s): Juan F. Quintana, Juan A. Bueren-Calabuig, Fabio Zuccotto, Harry P. de Koning, David Horn, Mark C. Field
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pntd.0002837

Discovery and Confirmation of Ligand Binding Specificities of the Schistosoma japonicum Polarity Protein Scribble
Cited by: 5
Author(s): Pengfei Cai, Yi Mu, Xiangshu Piao, Nan Hou, Shuai Liu, Youhe Gao, Heng Wang, Qijun Chen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pntd.0007687

Intestinal UDP-glucuronosyltransferase as a potential target for the treatment and prevention of lymphatic filariasis
Cited by: 10
Author(s): Alexander F. Flynn, Michael Joyce, Roger R. Taylor, Sasisekhar Bennuru, Alyssa R Lindrose, Spencer L Sterling, C. Paul Morris, Thomas B. Nutman, Edward Mitre
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0148174

On Nature’s Strategy for Assigning Genetic Code Multiplicity
Cited by: 16
Author(s): Simone Gardini, Sara Cheli, Silvia Baroni, Gabriele Di Lascio, Guido Mangiavacchi, Nicholas Micheletti, Carmen Luigia Monaco, L. Savini, Davide Alocci, Stefano Mangani, Neri Niccolai
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0161663

Amlexanox Blocks the Interaction between S100A4 and Epidermal Growth Factor and Inhibits Cell Proliferation
Cited by: 14
Author(s): Ching Chang Cho, Ruey Hwang Chou, Chin Yu
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0187845

Structural and kinetic considerations on the catalysis of deoxyarbutin by tyrosinase
Cited by: 7
Author(s): Antonio García‐Jiménez, José A. Teruel, Pedro Antonio Garcı́a-Ruiz, Adrian Saura‐Sanmartin, José Berná, Francisco Garcı́a-Cánovas, José Neptuno Rodríguez-López
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0068863

The N276 Glycosylation Site Is Required for HIV-1 Neutralization by the CD4 Binding Site Specific HJ16 Monoclonal Antibody
Cited by: 43
Author(s): Sunita S. Balla-Jhagjhoorsingh, Davide Corti, Leo Heyndríckx, Elisabeth Willems, Katleen Vereecken, David A. Davis, Guido Vanham
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0033698

Structural Basis of Ets1 Cooperative Binding to Widely Separated Sites on Promoter DNA
Cited by: 18
Author(s): Nigar D. Babayeva, Oxana I. Baranovskaya, T.H. Tahirov
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0116514

Novel ENAM and LAMB3 Mutations in Chinese Families with Hypoplastic Amelogenesis Imperfecta
Cited by: 24
Author(s): Xin Wang, Yuming Zhao, Yue Yuan, Man Qin
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0249905

Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP
Cited by: 2
Author(s): Shivani Ahuja, James Cahill, Kimberly Hartfield, Matthew R. Whorton
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0069538

Structure of the SCAN Domain of Human Paternally Expressed Gene 3 Protein
Cited by: 10
Author(s): V. Rimsa, T.C. Eadsforth, William N. Hunter
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0235642

Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity
Cited by: 24
Author(s): Antonielle Vieira Monclaro, Dejan M. Petrović, Gabriel Sérgio Costa Alves, Marcos M. C. Costa, G. E. O. Midorikawa, Robert G. Miller, Edivaldo Ximenes Ferreira Filho, Vincent G. H. Eijsink, Anikó Várnai
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0000531

Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry
Cited by: 13
Author(s): Qi Wang, Yuan Ping Pang
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0031677

Investigating the Structural Impacts of I64T and P311S Mutations in APE1-DNA Complex: A Molecular Dynamics Approach
Cited by: 43
Author(s): George Priya Doss C, N. Nagasundaram
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0032805

Inflammation-Associated Nitrotyrosination Affects TCR Recognition through Reduced Stability and Alteration of the Molecular Surface of the MHC Complex
Cited by: 18
Author(s): Chaithanya Madhurantakam, Adil Doğanay Duru, T. Sandalova, John R. Webb, Adnane Achour
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0137952

Methylatable Signaling Helix Coordinated Inhibitory Receiver Domain in Sensor Kinase Modulates Environmental Stress Response in Bacillus Cereus
Cited by: 5
Author(s): Jung-Chi Chen, Jyung-Hurng Liu, Duen-Wei Hsu, Jinian Shu, Chien‐Yen Chen, Chien‐Cheng Chen
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0025312

Determinants of Nucleotide-Binding Selectivity of Malic Enzyme
Cited by: 10
Author(s): Ju-Yi Hsieh, Mengchun Chen, Hui‐Chih Hung
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0169627

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA
Cited by: 4
Author(s): Bo Lin, Chin Yu Chen, Chih-Hsien Huang, Tzu Ping Ko, Cheng‐Hung Chiang, Kuan-Fu Lin, Yuan-Chih Chang, Po‐Yen Lin, Hui Lien Tsai, Andrew H.-J. Wang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0123441

Native Variants of the MRB1 Complex Exhibit Specialized Functions in Kinetoplastid RNA Editing
Cited by: 19
Author(s): Bhaskara Reddy Madina, Vijoy Kumar, Blaine H. M. Mooers, Jorge Cruz‐Reyes
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0003685

Evolutionary Patterning: A Novel Approach to the Identification of Potential Drug Target Sites in Plasmodium falciparum
Cited by: 13
Author(s): Pierre Durand, Kubendran Naidoo, Thérèsa L. Coetzer
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0046881

Role of the NC-Loop in Catalytic Activity and Stability in Lipase from Fervidobacterium changbaicum
Cited by: 15
Author(s): Binchun Li, Guangyu Yang, Lie Wu, Yan Feng
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0044480

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations
Cited by: 36
Author(s): Casper Steinmann, Mikael W. Ibsen, Anne S. Hansen, Jan H. Jensen
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0102389

The Structure of the TFIIH p34 Subunit Reveals a Von Willebrand Factor A Like Fold
Cited by: 10
Author(s): Dominik Schmitt, Jochen Kuper, Agnes Elias, Caroline Kisker
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0162344

Gonadotropins in the Russian Sturgeon: Their Role in Steroid Secretion and the Effect of Hormonal Treatment on Their Secretion
Cited by: 28
Author(s): Sue S. Yom, Lian Hollander-Cohen, Joseph Aizen, Benjamin Böhm, Michal Shpilman, Matan Golan, Avshalom Hurvitz, Gad Degani, Berta Levavi‐Sivan
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0084902

Adaptation of an L-Proline Adenylation Domain to Use 4-Propyl-L-Proline in the Evolution of Lincosamide Biosynthesis
Cited by: 19
Author(s): Stanislav Kadlčík, Tomáš Kučera, Dominika Chalupská, Radek Gažák, Markéta Koběrská, Dana Ulanová, Jan Kopecký, Eva Kutějová, Lucie Najmanová, Jiřı́ Janata
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0015258

Modifying the Substrate Specificity of Carcinoscorpius rotundicauda Serine Protease Inhibitor Domain 1 to Target Thrombin
Cited by: 5
Author(s): Pankaj K. Giri, Xuhua Tang, Saravanan Thangamani, Rajesh T. Shenoy, Jeak Ling Ding, Kunchithapadam Swaminathan, J. Sivaraman
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0136509

Designing Second Generation Anti-Alzheimer Compounds as Inhibitors of Human Acetylcholinesterase: Computational Screening of Synthetic Molecules and Dietary Phytochemicals
Cited by: 24
Author(s): Hafsa Amat-ur-Rasool, Mehboob Ahmed
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0052848

A Novel B-Cell Epitope Identified within Mycobacterium tuberculosis CFP10/ESAT-6 Protein
Cited by: 11
Author(s): Hua Yang, Haizhen Chen, Liu Z, Hui Ma, Lianhua Qin, Ruiliang Jin, Ruijuan Zheng, Yonghong Feng, Zhenling Cui, Jie Wang, Jinming Liu, Zhongyi Hu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0025365

Structural Insights into the Mechanism of Protein O-Fucosylation
Cited by: 84
Author(s): Erandi Lira‐Navarrete, Jessika Valero‐González, Raquel Villanueva, Marta Martínez‐Júlvez, Tomás Tejero, Pedro Merino, Santosh Panjikar, R. Hurtado‐Guerrero
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0020535

Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
Cited by: 7
Author(s): Tiina A. Riihimäki, Sampo Kukkurainen, Suvi Varjonen, Jarno Hörhä, Thomas K.M. Nyholm, Markku S. Kulomaa, Vesa P. Hytönen
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0012591

Reassortant between Human-Like H3N2 and Avian H5 Subtype Influenza A Viruses in Pigs: A Potential Public Health Risk
Cited by: 22
Author(s): Cong Yu, Guangmei Wang, Guan Zhang, Shuang Chang, Quanpeng Zhang, Genhua Yang, Weili Wang, Qing-Feng Meng, Weiming Ren, Chunfeng Wang, Zhuang Ding
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0102407

Annexin5 Plays a Vital Role in Arabidopsis Pollen Development via Ca2+-Dependent Membrane Trafficking
Cited by: 37
Author(s): Jingen Zhu, Xianghua Wu, Shunjie Yuan, Dong Qian, Qiong Nan, Lizhe An, Yun Xiang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0059411

Multiple Roles of the Extracellular Vestibule Amino Acid Residues in the Function of the Rat P2X4 Receptor
Cited by: 17
Author(s): Milos B. Rokic, Stanko S. Stojilković, Vojtěch Vávra, Pavlo Kuzyk, Vendula Tvrdoňová, Hana Zemková
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0059873

The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering
Cited by: 18
Author(s): Kyle T. Greenway, Eric B. LeGresley, B. Mario Pinto
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0011708

Adhesion and Degranulation Promoting Adapter Protein (ADAP) Is a Central Hub for Phosphotyrosine-Mediated Interactions in T Cells
Cited by: 36
Author(s): Marc Sylvester, Stefanie Kliche, Sabine S. Lange, Sabine Geithner, Clementine Klemm, Andreas Schlösser, Arndt Großmann, Ulrich Stelzl, Burkhart Schraven, Eberhard Krause, Christian Freund
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0192512

A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding
Cited by: 6
Author(s): Mingqin Wu, John J. Alvarado, Corinne E. Augelli‐Szafran, Roger G. Ptak, Thomas E. Smithgall
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0108607

Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels
Cited by: 23
Author(s): Parker W. de Waal, Kyle F. Sunden, Laura Lowe Furge
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0023507

Molecular Basis for the Recognition of Adenomatous Polyposis Coli by the Discs Large 1 Protein
Cited by: 26
Author(s): Zhenyi Zhang, Hua Li, Leyi Chen, Xingyu Lu, Jian Zhang, Ping Xu, Kui Lin, Geng Wu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0163816

Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI
Cited by: 8
Author(s): Mengchen Zhao, Heng Zhang, Guangfeng Liu, Li Wang, Jian Wang, Zengqiang Gao, Yuhui Dong, Linbo Zhang, Yong Gong
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0108245

Crystal Structure of Patatin-17 in Complex with Aged and Non-Aged Organophosphorus Compounds
Cited by: 17
Author(s): Sanjeeva J. Wijeyesakere, Rudy J. Richardson, Jeanne A. Stuckey
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0050011

Influence of Structural Symmetry on Protein Dynamics
Cited by: 14
Author(s): Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, J.R.H. Tame, Akinori Kidera
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0034541

Identification and Functional Characterisation of Novel Glucokinase Mutations Causing Maturity-Onset Diabetes of the Young in Slovakia
Cited by: 22
Author(s): Lucia Valentínová, Nicola L. Beer, Juraj Staník, Nicholas D. Tribble, Martijn van de Bunt, M Hučková, Amy Barrett, I Klimeš, Daniela Gašperíková, Anna L. Gloyn
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0071657

Soluble Variants of Human Recombinant Glutaminyl Cyclase
Cited by: 4
Author(s): Cristiana Castaldo, Silvia Ciambellotti, Raquel de Pablo-Latorre, Daniela Lalli, Valentina Porcari, Paola Turano
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0126725

Corosolic Acid Inhibits Hepatocellular Carcinoma Cell Migration by Targeting the VEGFR2/Src/FAK Pathway
Cited by: 40
Author(s): Ku Chung-Yu, Wang Ying-Ren, Lin H, Shao‐Chun Lu, Jung‐Yaw Lin
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0001926

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
Cited by: 32
Author(s): Hongbo Zhu, Iris E. Sommer, Thomas Lengauer, Francisco S. Domingues
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0123303

Improved Catenated Structures of Bovine Peroxiredoxin III F190L Reveal Details of Ring-Ring Interactions and a Novel Conformational State
Cited by: 9
Author(s): Zhenbo Cao, Donna P. McGow, Colin Shepherd, J. Gordon Lindsay
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0001310

Exchanging Murine and Human Immunoglobulin Constant Chains Affects the Kinetics and Thermodynamics of Antigen Binding and Chimeric Antibody Autoreactivity
Cited by: 38
Author(s): Marcela Torres, Narcís Fernández-Fuentes, András Fiser, Arturo Casadevall
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0052225

Structural Insights into Cellulolytic and Chitinolytic Enzymes Revealing Crucial Residues of Insect β-N-acetyl-D-hexosaminidase
Cited by: 16
Author(s): Tian Liu, Yong Zhou, Lei Chen, Wei Chen, L. Liu, Xu Shen, Wenqing Zhang, Jianzhen Zhang, Qing Yang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0039261

Intrinsically Unstructured Domain 3 of Hepatitis C Virus NS5A Forms a “Fuzzy Complex” with VAPB-MSP Domain Which Carries ALS-Causing Mutations
Cited by: 40
Author(s): Garvita Gupta, Haina Qin, Jianxing Song
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0133372

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions
Cited by: 24
Author(s): Stephen A. Wells, Marc W. van der Kamp, John D. McGeagh, Adrian J. Mulholland
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0022779

A Single Amino Acid of Human Immunodeficiency Virus Type 2 Capsid Protein Affects Conformation of Two External Loops and Viral Sensitivity to TRIM5α
Cited by: 21
Author(s): Tadashi Miyamoto, Masahiro Yokoyama, Ken Kono, Tatsuo Shioda, Hironori Sato, Emi E. Nakayama
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0074347

Allosteric Coupling between the Intracellular Coupling Helix 4 and Regulatory Sites of the First Nucleotide-binding Domain of CFTR
Cited by: 29
Author(s): Jennifer E. Dawson, Patrick Farber, Julie D. Forman-Kay
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0057345

Solution Structure of the QUA1 Dimerization Domain of pXqua, the Xenopus Ortholog of Quaking
Cited by: 3
Author(s): Mohsin Ali, R. William Broadhurst
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0149228

Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue
Cited by: 19
Author(s): Piyanat Meekrathok, Wipa Suginta
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0005058

Conservation of Carbohydrate Binding Interfaces — Evidence of Human HBGA Selection in Norovirus Evolution
Cited by: 109
Author(s): Ming Tan, Ming Xia, Yutao Chen, Weiming Bu, Rashmi S. Hegde, Jarosław Meller, Xuemei Li, Xi Jiang
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0077837

Combinatorial Engineering of Dextransucrase Specificity
Cited by: 16
Author(s): Romain Irague, Laurence Tarquis, Isabelle André, Claire Moulis, Sandrine Morel, Pierre Monsan, Gabrielle Potocki-Véronèse, Magali Remaud‐Siméon
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0234207

Client processing is altered by novel myopathy-causing mutations in the HSP40 J domain
Cited by: 4
Author(s): Melanie Y. Pullen, Conrad C. Weihl, Heather L. True
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0023032

A Crystal Structure of the Catalytic Core Domain of an Avian Sarcoma and Leukemia Virus Integrase Suggests an Alternate Dimeric Assembly
Cited by: 12
Author(s): Allison Ballandras, Karen Moreau, Xavier Robert, Marie-Pierre Confort, Romain Merceron, R. Haser, Corinne Ronfort, Patrice Gouet
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0032498

Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization
Cited by: 34
Author(s): Monica A. Totir, Nathaniel Echols, Max H. Nanao, Christine L. Gee, Alisa Moskaleva, Scott Gradia, Anthony T. Iavarone, James M. Berger, Andrew P. May, Chloé Zubieta, Tom Alber
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0012713

Molecular Modeling-Based Evaluation of hTLR10 and Identification of Potential Ligands in Toll-Like Receptor Signaling
Cited by: 78
Author(s): Rajiv Gandhi Govindaraj, Balachandran Manavalan, Gwang Lee, Sangdun Choi
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0091145

Engineering of Pyranose Dehydrogenase for Increased Oxygen Reactivity
Cited by: 17
Author(s): Iris Krondorfer, Katharina Lipp, Dagmar Brugger, Petra Staudigl, Christoph Sygmund, Dietmar Haltrich, Clemens K. Peterbauer
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0186277

Substitutions in conserved regions preceding and within the linker affect activity and flexibility of tRNase ZL, the long form of tRNase Z
Cited by: 2
Author(s): Makenzie Saoura, Kyla Pinnock, Maria Pujantell-Graell, Louis Levinger
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0001815

The Assembly of the Plasmodial PLP Synthase Complex Follows a Defined Course
Cited by: 21
Author(s): Ingrid Müller, Julia Knöckel, Matthew R. Groves, Rositsa Jordanova, S.E. Ealick, Rolf D. Walter, Carsten Wrenger
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0126565

In Silico and In Vitro Analysis of Bacoside A Aglycones and Its Derivatives as the Constituents Responsible for the Cognitive Effects of Bacopa monnieri
Cited by: 58
Author(s): Seetha Ramasamy, Sek Peng Chin, Sri Devi Sukumaran, Michael J. C. Buckle, Lik Voon Kiew, Lip Yong Chung
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0059142

Optimization of the Capsid of Recombinant Adeno-Associated Virus 2 (AAV2) Vectors: The Final Threshold?
Cited by: 84
Author(s): George Aslanidi, Angela Rivers, Luis A. Ortiz, Liujiang Song, Ling Chen, Lakshmanan Govindasamy, Kim Van Vliet, Tan Ming, Mavis Agbandje‐McKenna, Arun Srivastava
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0070005

Analysis of Adaptation Mutants in the Hemagglutinin of the Influenza A(H1N1)pdm09 Virus
Cited by: 18
Author(s): Alicia Jiménez-Alberto, Esmeralda Alvarado-Facundo, Rosa María Ribas‐Aparicio, Juan Arturo Castelán-Vega
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0037251

Computational Predictions of Volatile Anesthetic Interactions with the Microtubule Cytoskeleton: Implications for Side Effects of General Anesthesia
Cited by: 52
Author(s): Travis J. A. Craddock, Marc St. George, Holly Freedman, Khaled Barakat, Sambasivarao Damaraju, Stuart R. Hameroff, Jack A. Tuszyński
Software Mentions: 1
Published: about 14 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: almost 11 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

10.1371/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: almost 15 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

10.1371/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: about 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

10.1371/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: about 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: over 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

10.1371/journal.pone.0130394

MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria
Cited by: 17
Author(s): N. Zeytuni, Samuel Cronin, Christopher T. Lefèvre, Pascal Arnoux, Dror Baran, Zvi Shtein, Geula Davidov, Raz Zarivach
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0209230

Glucosylceramide acyl chain length is sensed by the glycolipid transfer protein
Cited by: 12
Author(s): Anders P. E. Backman, Josefin Halin, Henrik Nurmi, Anna Möuts, Matti A. Kjellberg, Peter Mattjus
Software Mentions: 1
Published: over 7 years ago