10.1128/JVI.00828-17

Cooperation between Strain-Specific and Broadly Neutralizing Responses Limited Viral Escape and Prolonged the Exposure of the Broadly Neutralizing Epitope
Cited by: 35
Author(s): Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil. Ferreria, Nigel Garrett, Salim S. Abdool Karim, Lynn Morris, Natasha T. Wood, Penny L. Moore, Carolyn Williamson
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2105-15-87

Estimation of protein function using template-based alignment of enzyme active sites
Cited by: 13
Author(s): Brett R. Hanson, Charles Westin, Mario De Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L. MacDonald, Greg J. Dodge, Paule M Boli, Cyprian Corwin, Haeja Kessler, Talia McKay, H. J. Bernstein, P. Craig
Software Mentions: 3
Published: over 12 years ago

10.1186/s12859-016-0898-8

Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Cited by: 22
Author(s): Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf‐Dieter Schubert, Alan Christoffels
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-10-153

Tableau-based protein substructure search using quadratic programming
Cited by: 11
Author(s): Alex Stivala, Anthony Wirth, Peter J. Stuckey
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-13-S14-S13

High-Throughput parallel blind Virtual Screening using BINDSURF
Cited by: 142
Author(s): Irene Sánchez-Linares, Horacio Pérez‐Sánchez, José M. Cecilia, José M. García
Software Mentions: 3
Published: about 14 years ago

10.1107/S1744309113013249

ErpC, a member of the complement regulator-acquiring family of surface proteins from<i>Borrelia burgdorferi</i>, possesses an architecture previously unseen in this protein family
Cited by: 13
Author(s): Joseph Caesar, Steven Johnson, Peter Kraiczy, Susan M. Lea
Software Mentions: 3
Published: over 13 years ago

10.6026/97320630015784

Molecular docking based virtual screening of the breast cancer target NUDT5
Cited by: 6
Author(s): Razia Sultana, Monjia Islam, Md Azizul Haque, Fatematuz Zuhura Evamoni, Zahid Mohammad Imran, Jabunnesa Khanom, Adnan Munim
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0257206

Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease
Cited by: 4
Author(s): R. V. Sriram Uday, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Samir Kumar Pal, V. Ravichandiran, Nakul C. Maiti
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1009431

High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19
Cited by: 29
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 5 years ago

10.1038/srep38564

Structure and dynamics of a constitutively active neurotensin receptor
Cited by: 55
Author(s): Brian E. Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F. White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 9 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase <i>Ce</i>Cht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-11-446

Fast and accurate protein substructure searching with simulated annealing and GPUs
Cited by: 44
Author(s): Alex Stivala, Peter J. Stuckey, Anthony Wirth
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0246915

Experimental and molecular predictions of the adjuvanticity of snail mucin on hepatitis B vaccine in albino mice
Cited by: 2
Author(s): Parker Elijah Joshua, Cynthia Ogochukwu Nwauzor, Damian Chukwu Odimegwu, Uzochukwu Gospel Ukachukwu, Rita Onyekachukwu Asomadu, Timothy Prince Chidike Ezeorba
Software Mentions: 3
Published: about 5 years ago

10.1093/jxb/eru266

Experimental and bioinformatic characterization of a recombinant polygalacturonase-inhibitor protein from pearl millet and its interaction with fungal polygalacturonases
Cited by: 8
Author(s): S. Prabhu, Ratna Singh, Stephan Kolkenbrock, Neerakkal Sujeeth, Nour Eddine El Gueddari, Bruno M. Moerschbacher, K. Ramachandra Kini, Martin Wagenknecht
Software Mentions: 3
Published: over 12 years ago

10.1186/s13321-019-0354-7

Bayesian optimization for conformer generation
Cited by: 34
Author(s): Lucian Chan, Geoffrey Hutchison, Garrett M. Morris
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0232959

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability
Cited by: 7
Author(s): Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
Software Mentions: 3
Published: over 6 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: about 7 years ago

10.3390/medsci7060074

In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts
Cited by: 0
Author(s): P. Sneha, Urmi Shah, S. Balaji
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/ery353

Homology modeling and<i>in vivo</i>functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase
Cited by: 20
Author(s): Gilles Lekeux, Jean-Marc Crowet, Cécile Nouet, Marine Joris, Alice Jadoul, Bernard Bosman, Monique Carnol, Patrick Motté, Laurence Lins, Moreno Galleni, Marc Hanikenne
Software Mentions: 3
Published: almost 8 years ago

10.1083/jcb.202005130

SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase
Cited by: 4
Author(s): Shaowu Xue, Menglu Wang, Claudia Schaffner, Olga O. Nerusheva, Dean Clift, Christos Spanos, David A. Kelly, Michael H. Tatham, Andreas U. Wallek, Yehui Wu, Juri Rappsilber, A. Arockia Jeyaprakash, Zuzana Storchová, Ronald T. Hay, Adèle L. Marston
Software Mentions: 3
Published: over 5 years ago

10.1042/BJ20141324

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases
Cited by: 61
Author(s): Karen McLuskey, Jeremy C. Mottram
Software Mentions: 3
Published: over 11 years ago

10.1074/jbc.RA118.004469

Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: almost 8 years ago

10.1074/jbc.M117.806893

Negatively charged residues in the first extracellular loop of the L-type CaV1.2 channel anchor the interaction with the CaVα2δ1 auxiliary subunit
Cited by: 16
Author(s): Benoîte Bourdin, Julie Briot, Marie-Philippe Tétreault, Rémy Sauvé, Lucie Parent
Software Mentions: 3
Published: about 9 years ago

10.1007/s00044-021-02715-8

n-Propyl 6-amino-2,6-dideoxy-2,2-difluoro-β-d-glucopyranoside is a good inhibitor for the β-galactosidase from E. coli
Cited by: 2
Author(s): Immo Serbian, Erik Prell, Cornelius Fischer, Hans‐Peter Deigner, René Csuk
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: over 9 years ago

10.1186/s13321-016-0157-z

Ligand-based virtual screening interface between PyMOL and LiSiCA
Cited by: 9
Author(s): Athira Athira, Samo Lešnik, Tanja Štular, Dušanka Janežič, Janez Konc
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.ppat.1008476

Past and ongoing adaptation of human cytomegalovirus to its host
Cited by: 18
Author(s): Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell’Oste, Chiara Pontremoli, Chiara Vantaggiato, Diego Forni, Mario Clerici, Santo Landolfo, Manuela Sironi
Software Mentions: 3
Published: over 6 years ago

10.1074/jbc.M114.621789

Complex Structure and Biochemical Characterization of the Staphylococcus aureus Cyclic Diadenylate Monophosphate (c-di-AMP)-binding Protein PstA, the Founding Member of a New Signal Transduction Protein Family
Cited by: 47
Author(s): Ivan Campeotto, Yong Everett Zhang, Miroslav Mladenov, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: almost 12 years ago

10.3389/frobt.2018.00133

Authenticity, Interactivity, and Collaboration in VR Learning Games
Cited by: 9
Author(s): Meredith Thompson, Annie Wang, Dan Roy, Eric Klopfer
Software Mentions: 3
Published: almost 8 years ago

10.1074/jbc.M115.671586

Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolR
Cited by: 30
Author(s): Justyna Aleksandra Wojdyla, Erin E. Cutts, Renata Kaminska, Grigorios Papadakos, Jonathan T. S. Hopper, Phillip J. Stansfeld, David Staunton, Carol V. Robinson, Colin Kleanthous
Software Mentions: 3
Published: about 11 years ago

10.3389/fpls.2019.00466

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling
Cited by: 34
Author(s): Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.00293

Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis
Cited by: 17
Author(s): Marina Klemenčič, Johannes Asplund-Samuelsson, Marko Dolinar, Christiane Funk
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.00266

Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat
Cited by: 14
Author(s): Mariateresa Volpicella, Immacolata Fanizza, Claudia Leoni, Ágata Gadaleta, Domenica Nigro, B. Gattulli, Giacomo Mangini, Antonio Blanco, Luigi R. Ceci
Software Mentions: 3
Published: over 10 years ago

10.1074/jbc.M116.730382

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
Cited by: 14
Author(s): Marco Igor Valencia-Sánchez, Annia Rodríguez‐Hernández, Ruben Ferreira, Hugo A. Santamaría-Suárez, Marcelino Arciniega, Anne-Catherine Dock-Brégeon, Dino Moras, Brice Beinsteiner, Haydyn D. T. Mertens, Dmitri I. Svergun, Luis G. Brieba, Morten Grøtli, Alfredo Torres‐Larios
Software Mentions: 3
Published: over 10 years ago

10.1155/2021/6696012

Active Learning and the Potential of Neural Networks Accelerate Molecular Screening for the Design of a New Molecule Effective against SARS-CoV-2
Cited by: 3
Author(s): Yassine Rabhi, Makrem Mrabet, Farhat Fnaiech
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1005294

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 3
Published: almost 10 years ago

10.3389/fmolb.2020.603983

Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors
Cited by: 1
Author(s): Mariem Ghoula, Axelle Le Marec, Christophe Magnan, Hervé Le Stunff, Olivier Taboureau
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmolb.2021.711975

Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels
Cited by: 6
Author(s): Michael Bründl, Sarala Pellikan, Anna Stary-Weinzinger
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2016.01810

The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles
Cited by: 9
Author(s): Marcela Iara Rodrigues, Agnes Alessandra Sekijima Takeda, Juliana Pereira Bravo, Ivan de Godoy Maia
Software Mentions: 3
Published: almost 10 years ago

10.1074/jbc.M117.776476

Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab
Cited by: 57
Author(s): Anna M. Davies, Elizabeth G. Allan, Anthony H. Keeble, Jean Delgado, Benjamin P. Cossins, A.N. Mitropoulou, M.O.Y. Pang, Tom Ceska, Andrew J. Beavil, Graham Craggs, Marta Westwood, Alistair J. Henry, James M. McDonnell, Brian J. Sutton
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1008848

Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis
Cited by: 1
Author(s): Libang He, Hao Wang, Yang Liu, Mei Kang, Tao Li, Changcheng Li, Aiping Tong, Yuanfeng Zhu, Yingjie Song, Stephen J. Savarino, Michael G. Prouty, Di Xia, Rui Bao
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1002708

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří­ Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: almost 14 years ago

10.1038/s42003-020-01639-0

Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization
Cited by: 14
Author(s): Jonathan R. Macey, Stephan Pabinger, Charles G. Barbieri, Ella S. Buring, Vanessa L. González, Daniel G. Mulcahy, Dustin DeMeo, Lara Urban, Paul M Hime, Stefan Prost, Aaron N. Elliott, Neil J. Gemmell
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-018-0063-1

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope
Cited by: 6
Author(s): Bankala Krishnarjuna, Toshihiko Sugiki, Rodrigo Morales, Jeffrey Seow, Toshimichi Fujiwara, Karyn L. Wilde, Raymond S. Norton, Christopher A. MacRaild
Software Mentions: 3
Published: over 8 years ago

10.1038/s42003-020-01401-6

Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step
Cited by: 13
Author(s): Han Zhang, Yuchen Li, Jinglei Nie, Jie Ren, An‐Ping Zeng
Software Mentions: 3
Published: almost 6 years ago

10.1186/1754-6834-7-18

Close relationship of a novel Flavobacteriaceaeα-amylase with archaeal α-amylases and good potentials for industrial applications
Cited by: 28
Author(s): Chunfang Li, Miaofen Du, Bin Cheng, Lushan Wang, Xinqiang Liu, Cuiqing Ma, Chunyu Yang, Ping Xu
Software Mentions: 3
Published: over 12 years ago

10.1186/1756-0500-3-289

Dockomatic - automated ligand creation and docking
Cited by: 21
Author(s): Casey W. Bullock, Reed B. Jacob, Owen M. McDougal, Greg Hampikian, Tim Andersen
Software Mentions: 3
Published: almost 16 years ago

10.1186/s13104-015-1760-1

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.bpj.2018.09.002

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR
Cited by: 3
Author(s): Graham M. Saunders, Hannah E. Bruce Macdonald, Jonathan W. Essex, Syma Khalid
Software Mentions: 3
Published: about 8 years ago

10.1016/j.molcel.2020.04.012

Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork
Cited by: 100
Author(s): Domagoj Baretić, Michael Jenkyn-Bedford, Valentina Aria, Giuseppe Cannone, Mark Skehel, Joseph T.P. Yeeles
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0080947

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity
Cited by: 43
Author(s): T. Vognsen, Ingvar R. Möller, Ole Kristensen
Software Mentions: 3
Published: almost 13 years ago

10.3389/fphar.2017.00393

Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket
Cited by: 6
Author(s): Tamir Dingjan, Anne Imberty, Serge Pérez, Elizabeth Yuriev, Paul A. Ramsland
Software Mentions: 3
Published: over 9 years ago

10.1093/gbe/evu235

Albuminoid Genes: Evolving at the Interface of Dispensability and Selection
Cited by: 12
Author(s): Alessandra Mozzi, Diego Forni, Rachele Cagliani, Jacopo Vertemara, Nereo Bresolin, Manuela Sironi
Software Mentions: 3
Published: almost 12 years ago

10.1093/gbe/evaa095

Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains
Cited by: 3
Author(s): Cameron J. Weadick
Software Mentions: 3
Published: over 6 years ago

10.3390/ani10060963

Characterization of Endolysin LyJH307 with Antimicrobial Activity against Streptococcus bovis
Cited by: 8
Author(s): Hanbeen Kim, Hyo Gun Lee, Inhyuk Kwon, Jakyeom Seo
Software Mentions: 3
Published: over 6 years ago

10.1007/s13361-018-1910-5

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31
Cited by: 5
Author(s): Andrey Dyachenko, Sem Tamara, Albert J. R. Heck
Software Mentions: 3
Published: over 8 years ago

10.3390/molecules23112954

Molecular Modeling and In Vitro Studies of a Neutral Oxime as a Potential Reactivator for Acetylcholinesterase Inhibited by Paraoxon
Cited by: 15
Author(s): Reuel L. de Paula, Joyce S. F. D. de Almeida, Samir F. A. Cavalcante, Arlan da Silva Gonçalves, Alessandro B. C. Simas, Tanos C. C. França, Martin Vališ, Kamil Kuča, Eugenie Nepovimová, José Mauro Granjeiro
Software Mentions: 3
Published: almost 8 years ago

10.1111/mpp.12868

Comparative transcriptome profiling uncovers a <i>Lilium regale</i> NAC transcription factor, <i>LrNAC35</i>, contributing to defence response against cucumber mosaic virus and tobacco mosaic virus
Cited by: 25
Author(s): Daoyang Sun, Xinguo Zhang, Qingyu Zhang, Xiaotong Ji, Yuping Jia, Hong Wang, Lixin Niu, Yanlong Zhang
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0083496

Exploration of Virtual Candidates for Human HMG-CoA Reductase Inhibitors Using Pharmacophore Modeling and Molecular Dynamics Simulations
Cited by: 17
Author(s): Maeng-Hyun Son, Ayoung Baek, Sugunadevi Sakkiah, Chanin Park, John Strouboulis, Keun Woo Lee
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-24775-4

A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue
Cited by: 22
Author(s): Chih-Hung Chuang, Shean‐Jaw Chiou, Tian−Lu Cheng, Yeng‐Tseng Wang
Software Mentions: 3
Published: over 8 years ago

10.1186/1472-6807-6-4

Identification of similar regions of protein structures using integrated sequence and structure analysis tools
Cited by: 20
Author(s): Brandon Peters, Charles W. Moad, Eunseog Youn, Kris Buffington, Randy Heiland, Sean D. Mooney
Software Mentions: 3
Published: over 20 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0214440

A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases
Cited by: 17
Author(s): Nazmul H Khan, Anthony A. Bui, Yang Xiao, R. Bryan Sutton, Robert W. Shaw, Benjamin J. Wylie, Michael P. Latham
Software Mentions: 3
Published: over 7 years ago

10.3390/v12010105

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111
Cited by: 8
Author(s): Aaron E. Lin, William E. Diehl, Yíngyún Caì, Courtney Finch, Chidiebere Akusobi, Robert N. Kirchdoerfer, Laura Bollinger, Stephen F. Schaffner, Elizabeth Brown, Erica Ollmann Saphire, Kristian G. Andersen, Jens H. Kuhn, Jeremy Luban, Pardis C. Sabeti
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0196484

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches
Cited by: 71
Author(s): Abbas Khan, Muhammad Junaid, Aman Chandra Kaushik, Arif Ali, Syed Shujait Ali, Aamir Mehmood, Dong‐Qing Wei
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0022201

A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase
Cited by: 50
Author(s): Jesse D. Bloom, Jagannath S. Nayak, David Baltimore
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00454-21

A Novel Phage Infecting <i>Alteromonas</i> Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs
Cited by: 16
Author(s): Ruijie Ma, Jiayong Lai, Xiaowei Chen, Long Wang, Yue Yang, Shuzhen Wei, Nianzhi Jiao, Rui Zhang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0077995

Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes
Cited by: 52
Author(s): Guillaume Gotthard, Julien Hiblot, Daniel H. González, Mikael Elias, Éric Chabrière
Software Mentions: 3
Published: almost 13 years ago

10.1186/1472-6807-5-19

Natural history of S-adenosylmethionine-binding proteins
Cited by: 240
Author(s): Piotr Koźbiał, Arcady Mushegian
Software Mentions: 3
Published: about 21 years ago

10.1371/journal.pone.0182016

An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins
Cited by: 20
Author(s): Marcin Michalik, Marcella Orwick‐Rydmark, Michael Habeck, Vikram Alva, Thomas C. Arnold, Dirk Linke
Software Mentions: 3
Published: about 9 years ago

10.1111/febs.15514

Structure‐based design of peptides that trigger <i>Streptococcus pneumoniae</i> cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0248887

Production and characterization of antibody against Opisthorchis viverrini via phage display and molecular simulation
Cited by: 0
Author(s): Sitthinon Siripanthong, Anchalee Techasen, Chanin Nantasenamat, Aijaz Ahmad Malik, Paiboon Sithithaworn, Chanvit Leelayuwat, Amonrat Jumnainsong
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0243085

Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions
Cited by: 7
Author(s): Jin-Hyun Kim, Joo-Seok Park, Chang Kyu Lee, Min‐Gyun Jeong, Jiu Liang Xu, Yong-Soo Choi, Han‐Sung Jung, Hyunju Choi
Software Mentions: 3
Published: almost 6 years ago

10.3390/v11020167

Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus
Cited by: 25
Author(s): Wenyan Zhang, Letian Zhang, Wanting He, Xu Zhang, Baiqing Wen, Congcong Wang, Qiuhua Xu, Gairu Li, Jiyong Zhou, Michael Veit, Shuo Su
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.RA119.010697

Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cited by: 3
Author(s): Jaime L. Jensen, Beau D. Jernberg, Sangita C. Sinha, Christopher L. Colbert
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0023779

Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK
Cited by: 38
Author(s): Mónica Galiano, Paul‐Michael Agapow, Catherine Thompson, Steven G. Platt, Anthony Underwood, Joanna Ellis, Richard Myers, Jonathan Green, Maria Zambon
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0143245

Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex
Cited by: 9
Author(s): Reda Rawi, Khalid Kunji, Abdelali Haoudi, Halima Bensmail
Software Mentions: 3
Published: almost 11 years ago

10.3390/biom11040529

Interaction of Ligands for PET with the Dopamine D3 Receptor: In Silico and In Vitro Methods
Cited by: 6
Author(s): Chia-Ju Hsieh, Aladdin Riad, Ji Youn Lee, Kristoffer Sahlholm, Kuiying Xu, Robert R. Luedtke, Robert H. Mach
Software Mentions: 3
Published: over 5 years ago

10.3390/biom11030458

A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani
Cited by: 18
Author(s): Emmanuel Broni, Samuel K. Kwofie, Seth O. Asiedu, Whelton A. Miller, Michael D. Wilson
Software Mentions: 3
Published: over 5 years ago

10.1107/S205225251900246X

Subatomic resolution X-ray structures of green fluorescent protein
Cited by: 24
Author(s): Kiyotsugu Takaba, Yang Tai, Haruhiko Eki, Hoang Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.3001057

The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek’s disease virus peptides by using an unprecedented binding motif
Cited by: 11
Author(s): Samer Halabi, Michael Ghosh, Stefan Stevanović, Hans‐Georg Rammensee, Luca D. Bertzbach, Benedikt B. Kaufer, Martin C. Moncrieffe, Bernd Kaspers, Sonja Härtle, Jim Kaufman
Software Mentions: 3
Published: over 5 years ago

10.1186/1472-6807-11-33

Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria
Cited by: 5
Author(s): Yu Song, A. Vit, Sean R. A. Devenish, H. K. Mahanty, Aymelt Itzen, Roger S. Goody, Wulf Blankenfeldt
Software Mentions: 3
Published: about 15 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1007747

ProteinVR: Web-based molecular visualization in virtual reality
Cited by: 40
Author(s): Kevin C. Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0145053

Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans
Cited by: 57
Author(s): Aijaz Ahmad, Mohmmad Younus Wani, Amber Khan, Nikhat Manzoor, Julitha Molepo
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms221910493

Discovery and Validation of Lmj_04_BRCT Domain, a Novel Therapeutic Target: Identification of Candidate Drugs for Leishmaniasis
Cited by: 6
Author(s): José Peña-Guerrero, Celia Fernández-Rubio, Aroia Burguete-Mikeo, Rima El-Dirany, Alfonso T. García-Sosa, Paul A. Nguewa
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1008568

Rosetta design with co-evolutionary information retains protein function
Cited by: 10
Author(s): Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler
Software Mentions: 3
Published: over 5 years ago

10.1016/j.cell.2021.02.045

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0007868

Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance
Cited by: 93
Author(s): Yogesh Hooda, Mohammad Saiful Islam Sajib, Hafizur Rahman, Stephen P. Luby, Joseph Bondy‐Denomy, Mathuram Santosham, Jason R Andrews, Samir K. Saha, Senjuti Saha
Software Mentions: 3
Published: almost 7 years ago

10.3390/biom10050744

Structure–Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Campylobacter jejuni Chemoreceptor Tlp3
Cited by: 13
Author(s): Mohammad Firoz Khan, Mayra A. Machuca, Mohammad Mizanur Rahman, Cengiz Koç, Raymond S. Norton, Brian J. Smith, Anna Roujeinikova
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0006180

Inhibitors of Trypanosoma cruzi Sir2 related protein 1 as potential drugs against Chagas disease
Cited by: 9
Author(s): Luís Gaspar, Ross P.. Coron, Paul Kong Thoo Lin, David Costa, Begoña Pérez-Cabezas, Joana Tavares, Meritxell Roura-Ferrer, Isbaal Ramos, C. Ronin, Louise L. Major, Fabrice Ciesielski, Iain K. Pemberton, Jane MacDougall, Paola Ciapetti, Terry Smith, Anabela Cordeiro-da-Silva
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0080210

Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes
Cited by: 25
Author(s): Fabian Kurth, Kieran Rimmer, Lakshmanane Premkumar, Biswaranjan Mohanty, Wilko Duprez, Maria A. Halili, Stephen R. Shouldice, Begoña Heras, David P. Fairlie, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 3
Published: almost 13 years ago

10.3390/biom10091286

Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2
Cited by: 13
Author(s): Faez Iqbal Khan, Fakhrul Hassan, Razique Anwer, Jia‐Xun Feng, Dakun Lai
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0115082

Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites
Cited by: 10
Author(s): Wenjie Ye, Debajyoti Paul, Lina Gao, Jolita Šečkutė, R. Sangaiah, K. Jayaraj, Zhenfa Zhang, P.A. Kaminski, S.E. Ealick, Avram Gold, Louise M. Ball
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pntd.0004978

Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses
Cited by: 52
Author(s): Manuela Sironi, Diego Forni, Mario Clerici, Rachele Cagliani
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0167978

Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases
Cited by: 12
Author(s): Fábio K. Tamaki, Diorge P. Souza, Valquiria P. Souza, Cecília M. Ikegami, Chuck S. Farah, Sandro R. Marana
Software Mentions: 3
Published: almost 10 years ago