10.1128/mSphere.01131-20

Phosphorylation of the Canonical Histone H2A Marks Foci of Damaged DNA in Malaria Parasites
Cited by: 5
Author(s): Manish Goyal, Adina Heinberg, Vera Mitesser, Sofiya Kandelis-Shalev, Brajesh Kumar Singh, Ron Dzikowski
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0035030

The Threonine Protease Activity of Testes-Specific Protease 50 (TSP50) Is Essential for Its Function in Cell Proliferation
Cited by: 21
Author(s): Yuyin Li, Yongli Bao, Zhenbo Song, Luguo Sun, Ping Wu, Yu Zhang, Cong Fan, Yanxin Huang, Yin Wu, Chunlei Yu, Yu Sun, Lihua Zheng, Guan‐Nan Wang, Yuxin Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0190658

Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region
Cited by: 8
Author(s): Louis Hollingsworth, Anne M. Brown, Richard D. Gandour, David R. Bevan
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0148108

Oxidation of Phe454 in the Gating Segment Inactivates Trametes multicolor Pyranose Oxidase during Substrate Turnover
Cited by: 6
Author(s): Petr Halada, Dagmar Brugger, Jindřich Volc, Clemens K. Peterbauer, Christian Leitner, Dietmar Haltrich
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0026431

Bioinformatic Analysis of Pathogenic Missense Mutations of Activin Receptor Like Kinase 1 Ectodomain
Cited by: 13
Author(s): Claudia Scotti, Carla Olivieri, Laura Boeri, Cecilia Canzonieri, Federica Ornati, Elisabetta Buscarini, Fabio Pagella, Cesare Danesino
Software Mentions: 1
Published: almost 15 years ago

10.1093/bioinformatics/btz062

Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
Cited by: 46
Author(s): Judemir Ribeiro, Carlos Ríos-Vera, Francisco S. Melo, Andreas Schüller
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0066458

Biochemical Characterization of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136T
Cited by: 9
Author(s): Sean E. McGroty, Dhivya T. Pattaniyil, Delphine Patin, Didier Blanot, Arvind Ravichandran, Hisao Suzuki, Renwick C. J. Dobson, Michael A. Savka, André O. Hudson
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0001443

A Mitochondrial Kinase Complex Is Essential to Mediate an ERK1/2-Dependent Phosphorylation of a Key Regulatory Protein in Steroid Biosynthesis
Cited by: 105
Author(s): Cecilia Poderoso, Daniela P. Converso, Paula Maloberti, Alejandra Duarte, Isabel Neuman, Soledad Galli, Fabiana Cornejo Maciel, Cristina Paz, Marı́a Cecilia Carreras, Juan José Poderoso, Ernesto J. Podestá
Software Mentions: 1
Published: over 18 years ago

10.1093/bioinformatics/bty818

PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles
Cited by: 3
Author(s): Sebastian Stolzenberg
Software Mentions: 1
Published: almost 8 years ago

10.1128/mSphere.00736-20

A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. <i>piscicida</i> Cleaves the Peptidoglycan of Potentially Competing Bacteria
Cited by: 3
Author(s): Johnny Lisboa, Cassilda Pereira, Aline Rifflet, Juan Ayala, Mateus S. Terceti, Alba V Barca, Inês S. Rodrigues, Pedro José Barbosa Pereira, Carlos R. Osorio, Francisco García‐del Portillo, Ivo Gomperts Boneca, Ana do Vale, Nuno M.S. dos Santos
Software Mentions: 1
Published: over 5 years ago

10.1093/bioinformatics/bty834

Towards region-specific propagation of protein functions
Cited by: 6
Author(s): Da Chen Emily Koo, Richard Bonneau
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0000982

Conservation, Variability and the Modeling of Active Protein Kinases
Cited by: 55
Author(s): James D.R. Knight, Bin Qian, David C. Baker, Rashmi Kothary
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0107509

A Ubiquitin Shuttle DC-UbP/UBTD2 Reconciles Protein Ubiquitination and Deubiquitination via Linking UbE1 and USP5 Enzymes
Cited by: 3
Author(s): Aimin Song, Hui Ye, Yong-Guang Gao, Chen Zhou, Yuhang Zhang, Hong Yu Hu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0155180

Exome Sequencing of a Pedigree Reveals S339L Mutation in the TLN2 Gene as a Cause of Fifth Finger Camptodactyly
Cited by: 9
Author(s): Hao Deng, Sheng Deng, Hongbo Xu, Hua Deng, Yulan Chen, Lamei Yuan, Xiong Deng, Shengbo Yang, Liping Guan, Jianguo Zhang, Hong Yuan, Yi Guo
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0142313

Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA
Cited by: 6
Author(s): Soshichiro Nagano, Eiko Seki, Ting‐Yu Lin, Mikako Shirouzu, Shigeyuki Yokoyama, Jonathan G. Heddle
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0056467

Amide Proton Solvent Protection in Amylin Fibrils Probed by Quenched Hydrogen Exchange NMR
Cited by: 32
Author(s): Andrei T. Alexandrescu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0242109

Improved soluble expression and use of recombinant human renalase
Cited by: 6
Author(s): Clifford S. Morrison, Elena E. Paskaleva, Marvin A Rios, Thomas R Beusse, Elaina M Blair, Lucy Lin, James R Hu, Aidan H Gorby, David R. Dodds, William B. Armiger, Jonathan S. Dordick, Mattheos Koffas
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0029514

A Novel, “Double-Clamp” Binding Mode for Human Heme Oxygenase-1 Inhibition
Cited by: 23
Author(s): Mona N. Rahman, Jason Z. Vlahakis, Dragic Vukomanovic, Wallace Lee, Walter A. Szarek, Kanji Nakatsu, Zongchao Jia
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0150288

Mycobacterium tuberculosis Peptidyl-Prolyl Isomerases Also Exhibit Chaperone like Activity In-Vitro and In-Vivo
Cited by: 26
Author(s): Saurabh Pandey, Ashish Sharma, Deeksha Tripathi, Ashutosh Kumar, Mohd Khubaib, Manish Bhuwan, Tapan K. Chaudhuri, Seyed E. Hasnain, Nasreen Z. Ehtesham
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0047028

Structural and Enzymatic characterization of the lactonase SisLac from Sulfolobus islandicus
Cited by: 68
Author(s): Julien Hiblot, Guillaume Gotthard, Éric Chabrière, Mikael Elias
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0138438

Androgen and Progesterone Receptors Are Targets for Bisphenol A (BPA), 4-Methyl-2,4-bis-(P-Hydroxyphenyl)Pent-1-Ene—A Potent Metabolite of BPA, and 4-Tert-Octylphenol: A Computational Insight
Cited by: 49
Author(s): Mohd Rehan, Ejaz Ahmad, Ishfaq Ahmad Sheikh, Adel M. Abuzenadah, Ghazi A. Damanhouri, Osama S. Bajouh, Samera F. AlBasri, Mansour M. Assiri, M.A. Beg
Software Mentions: 1
Published: almost 11 years ago

10.1093/bioinformatics/btaa104

Michela<scp>Ngl</scp>o: sculpting protein views on web pages without coding
Cited by: 19
Author(s): Matteo P. Ferla, Alistair T. Pagnamenta, David Damerell, Jenny C. Taylor, Brian D. Marsden
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0015873

Structure-Based Mutational Analysis of eIF4E in Relation to sbm1 Resistance to Pea Seed-Borne Mosaic Virus in Pea
Cited by: 45
Author(s): J. Ashby, Clare E. M. Stevenson, Gavin E. Jarvis, David M. Lawson, Andrew J. Maule
Software Mentions: 1
Published: over 15 years ago

10.1128/mSphere.00977-20

Comprehensive Bioinformatic Assessments of the Variability of Neisseria gonorrhoeae Vaccine Candidates
Cited by: 10
Author(s): Benjamin I. Baarda, Ryszard A. Zielke, Alaina K. Holm, Aleksandra E. Sikora
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0149903

Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance
Cited by: 12
Author(s): Sakshi Khosa, A. Hoeppner, Holger Gohlke, Lutz Schmitt, Sander H. J. Smits
Software Mentions: 1
Published: over 10 years ago

10.1093/bioinformatics/btaa677

Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry
Cited by: 53
Author(s): Andy M. Lau, Jürgen Claesen, Kjetil Hansen, Argyris Politis
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0100797

QSAR and Docking Studies on Capsazepine Derivatives for Immunomodulatory and Anti-Inflammatory Activity
Cited by: 30
Author(s): Aparna Shukla, Pooja Sharma, Om Prakash, Mohinder Singh, Komal Kalani, Feroz Khan, Dnyaneshwar Umrao Bawankule, Suaib Luqman, Santosh K. Srivastava
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0223387

Structural mechanism for regulation of DNA binding of BpsR, a Bordetella regulator of biofilm formation, by 6-hydroxynicotinic acid
Cited by: 5
Author(s): William T. Booth, Ryan R. Davis, Rajendar Deora, Thomas Hollis
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0047665

The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases
Cited by: 73
Author(s): Jennifer Chow, Filip Kovačić, Yuliya Dall Antonia, Ulrich Krauß, Francesco Fersini, Christel Schmeisser, Benjamin Lauinger, Patrick Bongen, Jörg Pietruszka, Marlen Schmidt, Ina Menyes, Uwe T. Bornscheuer, Marrit Eckstein, Oliver Thum, Andreas Liese, Jochen Mueller‐Dieckmann, Karl‐Erich Jaeger, Wolfgang R. Streit
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0080393

Involvement of and Interaction between WNT10A and EDA Mutations in Tooth Agenesis Cases in the Chinese Population
Cited by: 48
Author(s): Huiying He, Dong Han, Hailan Feng, Hong Qu, Seng Song, Baojing Bai, Zhenting Zhang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0040846

Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms
Cited by: 25
Author(s): Keng‐Chang Tsai, Jhih-Wei Jian, Ei-Wen Yang, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun‐Bo Chen, Jeng-Yih Chang, Wen-Lian Hsu, An-Suei Yang
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0033416

Crystal Structure of Diedel, a Marker of the Immune Response of Drosophila melanogaster
Cited by: 17
Author(s): Franck Coste, Cordula Kemp, Vanessa Bobezeau, Charles Hétru, Christine Kellenberger, Jean‐Luc Imler, Alain Roussel
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0055650

Characterization of the N-Terminal Domain of BteA: A Bordetella Type III Secreted Cytotoxic Effector
Cited by: 5
Author(s): Chen Guttman, Geula Davidov, Hadassa Shaked, Sofiya Kolusheva, Ronit Bitton, Atish Ganguly, Jeff F. Miller, Jordan H. Chill, Raz Zarivach
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0022253

Single-Molecule Fluorescence Polarization Study of Conformational Change in Archaeal Group II Chaperonin
Cited by: 7
Author(s): Ryo Iizuka, Taro Ueno, Nobuhiro Morone, Takashi Funatsu
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0000685

Mutations in the UBIAD1 Gene, Encoding a Potential Prenyltransferase, Are Causal for Schnyder Crystalline Corneal Dystrophy
Cited by: 104
Author(s): Andrew Orr, Marie‐Pierre Dubé, Julien L. Marcadier, Haiyan Jiang, Antonio Federico, Stanley George, Christopher Seamone, David Q. Andrews, Paul Dubord, Simon Holland, Sylvie Provost, Vanessa Mongrain, Susan C. Evans, Brent Higgins, Sharen Bowman, Duane L. Guernsey, Mark E. Samuels
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0037645

Protein Sequence Alignment Analysis by Local Covariation: Coevolution Statistics Detect Benchmark Alignment Errors
Cited by: 19
Author(s): Russell J. Dickson, Gregory B. Gloor
Software Mentions: 1
Published: about 14 years ago

10.3390/ijms21124475

Norditerpenoids with Selective Anti-Cholinesterase Activity from the Roots of Perovskia atriplicifolia Benth.
Cited by: 12
Author(s): Sylwester Ślusarczyk, F. Sezer Senol Deniz, Renata Abel, Łukasz Pecio, Horacio Pérez‐Sánchez, José P. Cerón‐Carrasco, Helena den-Haan, Priyanka Banerjee, Robert Preißner, Edward Krzyżak, Wiesław Oleszek, İlkay Erdoğan Orhan, Adam Matkowski
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0180241

Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism
Cited by: 4
Author(s): Shannon E. Hill, Elaine Nguyen, Chiamaka U. Ukachukwu, Dana M. Freeman, Stephen Quirk, Raquel L. Lieberman
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0162273

GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism
Cited by: 3
Author(s): Alejandra Young, Uma Dandekar, Calvin Pan, Avery Sader, Jie Zheng, Richard A. Lewis, Débora B. Farber
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0031445

Protein-Protein Interactions in Clathrin Vesicular Assembly: Radial Distribution of Evolutionary Constraints in Interfaces
Cited by: 1
Author(s): Rupali A. Gadkari, Narayanaswamy Srinivasan
Software Mentions: 1
Published: over 14 years ago

10.1093/bioinformatics/bty968

BlendMol: advanced macromolecular visualization in Blender
Cited by: 28
Author(s): Jacob D. Durrant
Software Mentions: 1
Published: over 7 years ago

10.1128/mSphere.00444-21

<i>Toxoplasma gondii</i> Toxolysin 4 Contributes to Efficient Parasite Egress from Host Cells
Cited by: 3
Author(s): My Hang Huynh, Marijo S. Roiko, A. da S. Gomes, Ellyn N. Schinke, Alyssa B. Schultz, Swati Agrawal, Christine A Oellig, Travis Sexton, Jessica M. Beauchamp, Julie Laliberté, Komagal Kannan Sivaraman, Louis B. Hersh, Sheena McGowan, Vern B. Carruthers
Software Mentions: 1
Published: about 5 years ago

10.1186/s12920-021-01042-6

Deletion of 2 amino acids in IHH in a Japanese family with brachydactyly type A1
Cited by: 1
Author(s): Nozomu Ozaki, Hiroko Okuda, Hatasu Kobayashi, Kouji H. Harada, Sumiko Inoue, Shohab Youssefian, Akio Koizumi
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0079544

New Antimalarial Hits from Dacryodes edulis (Burseraceae) - Part I: Isolation, In Vitro Activity, In Silico “drug-likeness” and Pharmacokinetic Profiles
Cited by: 27
Author(s): Denis Zofou, Esther Laure Tematio, Fidele Ntie‐Kang, Mathieu Téné, Moses N. Ngemenya, Pierre Tane, Vincent P. K. Titanji
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0112902

Identification of Functionally Important Residues of the Rat P2X4 Receptor by Alanine Scanning Mutagenesis of the Dorsal Fin and Left Flipper Domains
Cited by: 9
Author(s): Vendula Tvrdoňová, Milos B. Rokic, Stanko S. Stojilković, Hana Zemková
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0240920

A highly active heparinase I from Bacteroides cellulosilyticus: Cloning, high level expression, and molecular characterization
Cited by: 4
Author(s): Liwei Gao, Hongtao Zhu, Caiyun Liu, Zhixiang Lv, Xue‐Gong Fan, Ye-Wang Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0074636

Frequency and Pattern of Heteroplasmy in the Complete Human Mitochondrial Genome
Cited by: 71
Author(s): Ariel Delgado Ramos, Cristina Santos, Ligia Mateiu, María del Mar González, Luis Álvarez, Luı́sa Azevedo, António Amorim, María Pilar Aluja
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0072718

NMR Structure of Temporin-1 Ta in Lipopolysaccharide Micelles: Mechanistic Insight into Inactivation by Outer Membrane
Cited by: 30
Author(s): Rathi Saravanan, M. S. Joshi, Harini Mohanram, Anirban Bhunia, Maria Luisa Mangoni, Surajit Bhattacharjya
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0229077

Novel EGFR ectodomain mutations associated with ligand-independent activation and cetuximab resistance in head and neck cancer
Cited by: 12
Author(s): Sindhu Nair, Hoa Q. Trummell, Rajani Rajbhandari, Nanda K. Thudi, Susan E. Nozell, Jason M. Warram, Christopher D. Willey, Eddy S. Yang, William J. Placzek, James A. Bonner, Markus Bredel
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0087963

Structural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36
Cited by: 30
Author(s): Tadashi Satoh, K. Suzuki, Takumi Yamaguchi, Koichi Kato
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0195558

Membrane permeabilizing amphiphilic peptide delivers recombinant transcription factor and CRISPR-Cas9/Cpf1 ribonucleoproteins in hard-to-modify cells
Cited by: 51
Author(s): Thomas Del’Guidice, Jean-Pascal Lepetit-Stoffaes, Louis-Jean Bordeleau, Jean Roberge, Vanessa Théberge, Coraline Lauvaux, Xavier Barbeau, Jessica Trottier, Vibhuti P. Davé, Denis‐Claude Roy, Bruno Gaillet, Alain Garnier, David R.P. Guay
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0123379

Structural Effects of Protein Aging: Terminal Marking by Deamidation in Human Triosephosphate Isomerase
Cited by: 18
Author(s): Ignacio De la Mora-De la Mora, Alfredo Torres‐Larios, Sergio Enríquez-Flores, Sara T. Méndez, Adriana Castillo-Villanueva, Saúl Gómez-Manzo, Gabriel López-Velázquez, Jaime Marcial-Quino, Angélica Torres-Arroyo, Itzhel García-Torres, Horacio Reyes‐Vivas, Jesús Oria-Hernández
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0066542

Functional Characterization of the Cardiac Ryanodine Receptor Pore-Forming Region
Cited by: 7
Author(s): Joanne Euden, Sammy A. Mason, Alan J. Williams
Software Mentions: 1
Published: about 13 years ago

10.1128/mSystems.00163-19

Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli
Cited by: 26
Author(s): Calum A. Pattrick, Joseph P. Webb, Jeffrey Green, Roy R. Chaudhuri, Mark O. Collins, David J. Kelly
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSystems.00397-19

The Formaldehyde Dehydrogenase SsFdh1 Is Regulated by and Functionally Cooperates with the GATA Transcription Factor SsNsd1 in Sclerotinia sclerotiorum
Cited by: 13
Author(s): Genglin Zhu, Gang Yu, Xianghui Zhang, Jinliang Liu, Yanhua Zhang, Jeffrey A. Rollins, Jingtao Li, Hongyu Pan
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12920-021-00884-4

A novel recessive PDZD7 bi-allelic mutation in an Iranian family with non-syndromic hearing loss
Cited by: 5
Author(s): Hossein Fahimi, Samira Behroozi, Sadaf Noavar, Farshid Parvini
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0023245

Structural Analysis of the Essential Resuscitation Promoting Factor YeaZ Suggests a Mechanism of Nucleotide Regulation through Dimer Reorganization
Cited by: 22
Author(s): Inci Aydin, Yumiko Saijo-Hamano, Keiichi Namba, Connor Thomas, Anna Roujeinikova
Software Mentions: 1
Published: almost 15 years ago

10.1093/bioinformatics/btt326

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet
Cited by: 44
Author(s): Alessandro Pandini, Arianna Fornili, Franca Fraternali, Jens Kleinjung
Software Mentions: 1
Published: about 13 years ago

10.3390/ijms21124234

Mono-PEGylation of a Thermostable Arginine-Depleting Enzyme for the Treatment of Lung Cancer
Cited by: 13
Author(s): Sai Fung Chung, Chi Fai Kim, Sui-Yi Kwok, Suet Ying Tam, Yu Wai Chen, Hiu Chi Chong, Sau Fong Leung, Pui‐Kin So, Kwok Yin Wong, Yun Chung Leung, Wai Hung Lo
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0069228

Disruption of Hydrogen Bonds between Major Histocompatibility Complex Class II and the Peptide N-Terminus Is Not Sufficient to Form a Human Leukocyte Antigen-DM Receptive State of Major Histocompatibility Complex Class II
Cited by: 12
Author(s): Monika-Sarah E. D. Schulze, Anne-Kathrin Anders, Dhruv Sethi, Melissa Call
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0038709

Mycobacterium tuberculosis DosR Regulon Gene Rv0079 Encodes a Putative, ‘Dormancy Associated Translation Inhibitor (DATIN)’
Cited by: 28
Author(s): Ashutosh Kumar, Mohammad Majid, Ralph Kunisch, Pittu Sandhya Rani, Insaf Ahmed Qureshi, Astrid Lewin, Seyed E. Hasnain, Niyaz Ahmed
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0007295

Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks
Cited by: 45
Author(s): М. А. Хаснатинов, Katarína Ustaníková, Т. В. Фролова, В В Погодина, Н. Г. Бочкова, Л С Левина, Mirko Slovák, Mária Kazimírová, М Лабуда, Boris Klempa, E Elecková, Ernest A. Gould, Т.С. Грицун
Software Mentions: 1
Published: almost 17 years ago

10.1128/mSystems.00705-19

The Remarkable Dual-Level Diversity of Prokaryotic Flagellins
Cited by: 11
Author(s): Dalong Hu, Peter R. Reeves
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21134678

Deciphering the Binding of Salicylic Acid to Arabidopsis thaliana Chloroplastic GAPDH-A1
Cited by: 8
Author(s): Igor Pokotylo, Denis Hellal, Tahar Bouceba, Miguel Ángel Hernández-Martínez, V. S. Kravets, Luís Leitão, Christophe Espinasse, Isabelle Kleiner, Éric Ruelland
Software Mentions: 1
Published: about 6 years ago

10.1128/mSystems.00821-20

Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism
Cited by: 20
Author(s): Ke Ma, Yu Feng, Alan McNally, Zhiyong Zong
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0256572

Human norovirus GII.4 Hong Kong variant shares common ancestry with GII.4 Osaka and emerged in Thailand in 2016
Cited by: 1
Author(s): Watchaporn Chuchaona, Jira Chansaenroj, Jiratchaya Puenpa, Sarawut Khongwichit, Sumeth Korkong, Sompong Vongpunsawad, Yong Poovorawan
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0073782

Insights into the Cross-Immunity Mechanism within Effector Families of Bacteria Type VI Secretion System from the Structure of StTae4-EcTai4 Complex
Cited by: 11
Author(s): H. Zhang, Zengqiang Gao, Yong Wei, Jianhua Xu, Yuhui Dong
Software Mentions: 1
Published: almost 13 years ago

10.3390/ijms21144979

Cationic Pillar[6]arene Induces Cell Apoptosis by Inhibiting Protein Tyrosine Phosphorylation Via Host–Guest Recognition
Cited by: 6
Author(s): Can-Peng Li, Yuxun Lu, Cheng-Ting Zi, Yuting Zhao, Hui Zhao, Yaping Zhang
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0028778

In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel
Cited by: 24
Author(s): Kirsten Knape, Tobias Linder, Peter Wolschann, Anton Beyer, Anna Stary-Weinzinger
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0048595

Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants
Cited by: 12
Author(s): Dongying Gao, José Carlos Jiménez-López, Akihisa Iwata, Navdeep Gill, Scott A. Jackson
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0192661

Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation
Cited by: 3
Author(s): Tobias Kromann-Hansen, E.L. Lange, Ida Katrine Lund, Gunilla Høyer‐Hansen, Peter A. Andreasen, Elizabeth A. Komives
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0025246

Using Shifts in Amino Acid Frequency and Substitution Rate to Identify Latent Structural Characters in Base-Excision Repair Enzymes
Cited by: 1
Author(s): Ramiro Barrantes-Reynolds, Susan S. Wallace, Jeffrey P. Bond
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0048360

Structural Insight into the Clostridium difficile Ethanolamine Utilisation Microcompartment
Cited by: 51
Author(s): Alison C. Pitts, Laura Tuck, Alexandra Faulds-Pain, Richard J. Lewis, Jon Marles‐Wright
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0198010

Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification
Cited by: 9
Author(s): K. Fukano, K. Ozawa, Masaya Kokubu, Tetsu Shimizu, Shinsaku Ito, Yasuyuki Sasaki, Akira Nakamura, Seishi Yajima
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0171328

Evidence for disulfide bonds in SR Protein Kinase 1 (SRPK1) that are required for activity and nuclear localization
Cited by: 18
Author(s): Maria Koutroumani, Γεώργιος Παπαδόπουλος, Metaxia Vlassi, Eleni Nikolakaki, Thomas Giannakouŕos
Software Mentions: 1
Published: over 9 years ago

10.1007/s00439-020-02150-6

Ethnogeographic and inter-individual variability of human ABC transporters
Cited by: 32
Author(s): Qingyang Xiao, Yitian Zhou, Volker M. Lauschke
Software Mentions: 1
Published: over 6 years ago

10.1007/s00439-019-02081-x

The genetic landscape of the human solute carrier (SLC) transporter superfamily
Cited by: 70
Author(s): L.C. Schaller, Volker M. Lauschke
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0007838

Inhibition of Neuraminidase Inhibitor-Resistant Influenza Virus by DAS181, a Novel Sialidase Fusion Protein
Cited by: 65
Author(s): Gallen Triana‐Baltzer, Larisa V. Gubareva, Alexander Klimov, David F. Wurtman, Ronald B. Moss, Maria Hedlund, Jeffrey Larson, Robert B. Belshe, Fang Fang
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0192826

Computer simulations reveal changes in the conformational space of the transcriptional regulator MosR upon the formation of a disulphide bond and in the collective motions that regulate its DNA-binding affinity
Cited by: 5
Author(s): Amanda Souza Câmara, E. Horjales
Software Mentions: 1
Published: over 8 years ago

10.1186/1479-7364-7-10

Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach
Cited by: 45
Author(s): C. George Priya Doss, N. Nagasundaram, Chiranjib Chakraborty, Luonan Chen, Hailong Zhu
Software Mentions: 1
Published: over 13 years ago

10.1186/1479-7364-6-10

Conservation of the three-dimensional structure in non-homologous or unrelated proteins
Cited by: 25
Author(s): Konstantinos Sousounis, Carl E Haney, Jian Cao, Bharath Sunchu, Panagiotis A. Tsonis
Software Mentions: 1
Published: about 14 years ago

10.1186/s40246-021-00351-2

Established and candidate transthyretin amyloidosis variants identified in the Saudi population by data mining
Cited by: 5
Author(s): Mohamed Abouelhoda, Dania Mohty, Islam Alayary, Brian F. Meyer, Stefan T. Arold, Bahaa M. Fadel, Dorota Monies
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0013105

Insight into Antigenic Diversity of VAR2CSA-DBL5ε Domain from Multiple Plasmodium falciparum Placental Isolates
Cited by: 18
Author(s): Sédami Gnidehou, Leon Eyrich Jessen, Stéphane Gangnard, Caroline Ermont, CHoukri Triqui, Mickäel Quiviger, Juliette Guitard, Ole Lund, Philippe Deloron, Nicaise Tuikue Ndam
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0014310

Co-Conserved Features Associated with cis Regulation of ErbB Tyrosine Kinases
Cited by: 14
Author(s): Asra Mirza, Morad Mustafa, Eric Talevich, Natarajan Kannan
Software Mentions: 1
Published: over 15 years ago

10.1186/s40246-021-00345-0

ACER3-related leukoencephalopathy: expanding the clinical and imaging findings spectrum due to novel variants
Cited by: 1
Author(s): Ali Zare Dehnavi, Erfan Heidari, Maryam Rasulinezhad, Morteza Heidari, Mahmoud Reza Ashrafi, Mohammad Mehdi Hosseini, Fatemeh Sadeghzadeh, Mohammad‐Sadegh Fallah, Noushin Rostampour, Amir Bahraini, Masoud Garshasbi, Ali Reza Tavasoli
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0096975

Structural Insights into the Evolution of a Sexy Protein: Novel Topology and Restricted Backbone Flexibility in a Hypervariable Pheromone from the Red-Legged Salamander, Plethodon shermani
Cited by: 17
Author(s): Damien B. Wilburn, Kathleen E. Bowen, Kari A. Doty, Sengodagounder Arumugam, Andrew N. Lane, Pamela W. Feldhoff, Richard C. Feldhoff
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0027989

Impact of Host Cell Line Adaptation on Quasispecies Composition and Glycosylation of Influenza A Virus Hemagglutinin
Cited by: 41
Author(s): Jana Roedig, Erdmann Rapp, Dirk W. Höper, Yvonne Genzel, Udo Reichl
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0196918

Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches
Cited by: 8
Author(s): Erika Piccirillo, Thiago Gerônimo Pires Alegria, Karen Fulan Discola, Jose A. R. R. Cussiol, Renato Mateus Domingos, Marcos Aurélio Farias de Oliveira, Leandro de Rezende, Luís Eduardo Soares Netto, Antonia T-do Amaral
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0132956

Folded or Not? Tracking Bet v 1 Conformation in Recombinant Allergen Preparations
Cited by: 5
Author(s): Felix Husslik, Kay-Martin Hanschmann, Ariane Krämer, Christian Seutter von Loetzen, Kristian Schweimer, Iris Bellinghausen, Regina Treudler, Jan C. Simon, Lothar Vogel, Elke Völker, Stefanie Randow, Andreas Reuter, Paul Rösch, Stefan Vieths, Thomas Holzhauser, Dirk Schiller
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0066913

Identification of Residues Involved in Substrate Specificity and Cytotoxicity of Two Closely Related Cutinases from Mycobacterium tuberculosis
Cited by: 15
Author(s): Luc Dedieu, Carole Serveau-Avesque, Stéphane Canaan
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0058297

The N-terminal Helix Controls the Transition between the Soluble and Amyloid States of an FF Domain
Cited by: 16
Author(s): Virginia Leyva Castillo, Fabrizio Chiti, Salvador Ventura
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0062697

Crystal Structure of Human TWEAK in Complex with the Fab Fragment of a Neutralizing Antibody Reveals Insights into Receptor Binding
Cited by: 18
Author(s): Alfred Lammens, Monika Baehner, Ulrich Kohnert, Jens Niewoehner, Leopold von Proff, Michael Schraeml, Katja Lammens, Karl‐Peter Hopfner
Software Mentions: 1
Published: over 13 years ago

10.1093/bioinformatics/btv458

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
Cited by: 52
Author(s): Francis Gaudreault, Louis‐Philippe Morency, Rafaël Najmanovich
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0021640

Crystal Structures of Histone and p53 Methyltransferase SmyD2 Reveal a Conformational Flexibility of the Autoinhibitory C-Terminal Domain
Cited by: 41
Author(s): Yuanyuan Jiang, Nualpun Sirinupong, J.S. Brunzelle, Zhe Yang
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0160345

Generation and Characterization of an IgG4 Monomeric Fc Platform
Cited by: 14
Author(s): Lu Shan, Magali Colazet, Kim Rosenthal, Xiang-Qing Yu, Jared S. Bee, Andrew D. Ferguson, Melissa Damschroder, Herren Wu, William F. Dall’Acqua, Ping Tsui, Vaheh Oganesyan
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0109521

Identification of a Novel Nucleocytoplasmic Shuttling RNA Helicase of Trypanosomes
Cited by: 14
Author(s): Alexandre Haruo Inoue, Mariana Serpeloni, Priscila Mazzocchi Hiraiwa, Sueli Fumie Yamada‐Ogatta, J.R.C. Muniz, María Cristina M. Motta, Newton Medeiros Vidal, Samuel Goldenberg, Andréa Rodrigues Ávila
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0187778

Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains
Cited by: 6
Author(s): Javier García-Pardo, Sebastián Tanco, Lucía Díaz, Sayani Dasgupta, Juan Fernández‐Recio, Júlia Lorenzo, Francesc X. Aviles, Lloyd D. Fricker
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0066211

An Experimental and Computational Evolution-Based Method to Study a Mode of Co-evolution of Overlapping Open Reading Frames in the AAV2 Viral Genome
Cited by: 14
Author(s): Yasuhiro Kawano, Shane Neeley, Kei Adachi, Hiroyuki Nakai
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0043761

Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein
Cited by: 6
Author(s): Abhinav Kumar, Sabine Möcklinghoff, Fumiaki Yumoto, Lukasz Jaroszewski, Carol L. Farr, Anna Grzechnik, Phuong Nguyen, Christian X. Weichenberger, Hsiu‐Ju Chiu, Heath E. Klock, Marc‐André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Bruce R. Conklin, Robert J. Fletterick, Ian A. Wilson
Software Mentions: 1
Published: almost 14 years ago

10.1093/bioinformatics/btx345

Protein–Sol: a web tool for predicting protein solubility from sequence
Cited by: 334
Author(s): Max Hebditch, Manuel Alejandro Carballo-Amador, Spyros Charonis, Robin Curtis, Jim Warwicker
Software Mentions: 1
Published: about 9 years ago