10.3389/fmicb.2020.582437

Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis
Cited by: 5
Author(s): M. Yamaguchi, Moe Takemura, Kõtarõ Higashi, Kana Goto, Yujiro Hirose, Tomoko Sumitomo, Masao Nakata, Narikazu Uzawa, Shigetada Kawabata
Software Mentions: 3
Published: about 6 years ago

10.1107/S1399004715004241

Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Cited by: 4
Author(s): Nader Morshed, Nathaniel Echols, Paul D. Adams
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2017.02034

Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria
Cited by: 10
Author(s): Hai‐Yan Cao, Peng Wang, Fei Xu, Ping‐Yi Li, Bin-Bin Xie, Qi‐Long Qin, Yuzhong Zhang, Chunyang Li, Xiu-Lan Chen
Software Mentions: 3
Published: almost 9 years ago

10.3389/fimmu.2021.664877

Ovine CD14- an Immune Response Gene Has a Role Against Gastrointestinal Nematode Haemonchus contortus—A Novel Report
Cited by: 6
Author(s): Kavita Rawat, Aruna Pal, Sandipan Banerjee, Abantika Pal, S. C. Mandal, Subhasis Batabyal
Software Mentions: 3
Published: about 5 years ago

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-017-08842-w

Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach
Cited by: 226
Author(s): Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2018.02086

The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy
Cited by: 6
Author(s): Alessandra Mozzi, Diego Forni, Mario Clerici, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2018.03353

Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases
Cited by: 35
Author(s): Masao Inoue, Issei Nakamoto, Kimiho Omae, Tatsuki Oguro, Hiroyuki Ogata, Takashi Yoshida, Yoshihiko Sako
Software Mentions: 3
Published: over 7 years ago

10.3389/fcvm.2020.00008

Protein Subdomain Enrichment of NUP155 Variants Identify a Novel Predicted Pathogenic Hotspot
Cited by: 2
Author(s): Riley J Leonard, Claudia C. Preston, Melanie E Gucwa, Yohannes Afeworki Tecleab, Arielle Selya, Randolph S. Faustino
Software Mentions: 3
Published: over 6 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

10.1016/j.febslet.2015.11.030

Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli
Cited by: 13
Author(s): Cristina Ortiz, Danguole Kureisaite-Ciziene, Florian Schmitz, Stephen H. McLaughlin, Miguel Vicente, Jan Löwe
Software Mentions: 3
Published: almost 11 years ago

10.3389/fcimb.2020.00082

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production
Cited by: 6
Author(s): Scott N. Dean, Morgan E. Milton, John Cavanagh, Monique L. van Hoek
Software Mentions: 3
Published: over 6 years ago

10.1107/S1744309113012931

Structure of PatF from<i>Prochloron didemni</i>
Cited by: 26
Author(s): Andrew F. Bent, Jesko Koehnke, Wael E. Houssen, Margaret Caroline MacHin Smith, Marcel Jaspars, James H. Naismith
Software Mentions: 3
Published: over 13 years ago

10.1107/S2059798320001679

<i>ALEPH</i>: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
Cited by: 15
Author(s): Ana María Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo Sammito
Software Mentions: 3
Published: over 6 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

10.1007/s00792-013-0542-8

The role of disulfide bond in hyperthermophilic endocellulase
Cited by: 13
Author(s): Han-Woo Kim, Kazuhiko Ishikawa
Software Mentions: 3
Published: over 13 years ago

10.12688/f1000research.12301.2

In silico analysis of natural compounds targeting structural and nonstructural proteins of chikungunya virus
Cited by: 16
Author(s): Jaspreet Jain, Anchala Kumari, Pallavi Somvanshi, Abhinav Grover, S. Somnath Pai, Sujatha Sunil
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcimb.2021.605589

Disseminated Talaromyces marneffei Infection in a Non-HIV Infant With a Homozygous Private Variant of RELB
Cited by: 9
Author(s): Xiaojuan Ding, Han Huang, Lili Zhao, Min Chen, Fang Peng, Bing Zhang, Xinyu Cui, Xiu‐An Yang
Software Mentions: 3
Published: over 5 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

10.7554/eLife.59753

Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host–pathogen conflict
Cited by: 29
Author(s): J.B. Eaglesham, Kacie McCarty, Philip J. Kranzusch
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0147097

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking
Cited by: 9
Author(s): Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jianli Wang, Tamar Schlick
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0182972

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight
Cited by: 8
Author(s): Leslie Regad, Jean-Baptiste Chéron, Dhoha Triki, Caroline Senac, Delphine Flatters, Anne-Claude Camproux
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0201509

Hydroxycholesterol binds and enhances the anti-viral activities of zebrafish monomeric c-reactive protein isoforms
Cited by: 11
Author(s): Melissa Belló-Pérez, Alberto Falcó, Beatriz Novoa, Luis Pérez, Julio Coll
Software Mentions: 3
Published: over 7 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

10.1371/journal.pone.0217164

Three genetically distinct ferlaviruses have varying effects on infected corn snakes (Pantherophis guttatus)
Cited by: 7
Author(s): Michael Pees, Volker Schmidt, Tibor Papp, Ákos Gellért, Maha Diekan Abbas, J. Matthias Starck, Annkatrin Neul, Rachel E. Marschang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0236894

A chemical interpretation of protein electron density maps in the worldwide protein data bank
Cited by: 5
Author(s): Sen Yao, Hunter N. B. Moseley
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0243429

A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations
Cited by: 2
Author(s): Dimitrios A. Mitsikas, Nicholas M. Glykos
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0043245

A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Cited by: 62
Author(s): Nemin Celik, Chaille T Webb, Denisse L. Leyton, Kathryn E. Holt, Eva Heinz, Rebecca J. Gorrell, Terry Kwok, Thomas Naderer, Richard A. Strugnell, Terence P. Speed, Rohan D. Teasdale, Vladimir A Likić, Trevor Lithgow
Software Mentions: 3
Published: about 14 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

10.1155/2013/185282

Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein
Cited by: 20
Author(s): Bikash R. Sahoo, Madhubanti Basu, Bichitrananda Swain, Manas Ranjan Dikhit, P. Jayasankar, Mrinal Samanta
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0150634

Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants
Cited by: 4
Author(s): Preeti Arya, Vishal Acharya
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-11-155

Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Cited by: 13
Author(s): Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0097817

Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning
Cited by: 12
Author(s): HyeonSeok Shin, Yoobok Cho, Donghui Choe, Yu‐Jin Jeong, Suhyung Cho, Sun Chang Kim, Byung-Kwan Cho
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0172743

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Cited by: 35
Author(s): Akshay Sridhar, Gregory A. Ross, Philip C. Biggin
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0082341

Targeting a Cross-Reactive Gly m 5 Soy Peptide as Responsible for Hypersensitivity Reactions in a Milk Allergy Mouse Model
Cited by: 21
Author(s): Renata Curciarello, Paola Lorena Smaldini, Ángela María Candreva, Vicente Ferreira González, Gustavo Parisi, Ana Cauerhff, Ivana Analía Barrios, Luis Enrique Bruno Blanch, Carlos A. Fossati, Silvana Petruccelli, Guillermo Horacio Docena
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0035974

The Hepatitis E Virus Polyproline Region Is Involved in Viral Adaptation
Cited by: 74
Author(s): Michael A. Purdy, James Lara, Yury Khudyakov
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-13-S4-S16

Intuitive representation of surface properties of biomolecules using BioBlender
Cited by: 59
Author(s): Raluca Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Pan, Monica Zoppè
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0241754

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak
Cited by: 9
Author(s): Fredrick Eyase, Solomon Langat, Irina Maljkovic Berry, Francis Mulwa, Albert Nyunja, James Mu, Samuel Owaka, Samson Limbaso, Victor Ofula, Hellen Koka, Edith Koskei, Joel Lutomiah, Richard G. Jarman, Rosemary Sang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0078059

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
Cited by: 25
Author(s): Kristóf Z. Szalay, Péter Csermely
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0199585

Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials
Cited by: 6
Author(s): John E. Holland, Qinxin Pan, Gevorg Grigoryan
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0102856

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective
Cited by: 23
Author(s): Ashutosh Srivastava, Somdatta Sinha
Software Mentions: 3
Published: about 12 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

10.1371/journal.pone.0029237

Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster
Cited by: 19
Author(s): Constância Flávia Junqueira Ayres, Pie Müller, Naomi Dyer, Craig S. Wilding, Daniel J. Rigden, Martin J. Donnelly
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0241513

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX
Cited by: 12
Author(s): Linda Yingqi Lin, Sawyer McCarthy, Barrett M. Powell, Yanti Manurung, Irene M. Xiang, William L. Dean, Brad Chaires, Liliya A. Yatsunyk
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1009651

Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity
Cited by: 6
Author(s): Aaron D. Besterman, Thorsten Althoff, Peter Elfferich, Irma Gutierrez-Mejia, Joshua Sadik, Jonathan A. Bernstein, Yvette van Ierland, Anja A. Kattentidt-Mouravieva, Mark Nellist, Jeff Abramson, Julián A. Martínez-Agosto
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0169687

Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO)
Cited by: 59
Author(s): Allison Cox, Benjamin W. Darbro, Ronald M. Laxer, Gabriel Vélez, Xinyu Bing, Alexis L. Finer, Albert Erives, Vinit B. Mahajan, Alexander G. Bassuk, Polly J. Ferguson
Software Mentions: 3
Published: over 9 years ago

10.1107/S0907444910000302

Rapid model building of β-sheets in electron-density maps
Cited by: 4
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 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

10.1186/1471-2105-13-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

10.1371/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

10.1371/journal.pcbi.1006722

Identifying individual risk rare variants using protein structure guided local tests (POINT)
Cited by: 8
Author(s): Rachel West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger‐Reif, Denis Fourches, Jung Ying Tzeng
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1008140

A steady-state model of microbial acclimation to substrate limitation
Cited by: 13
Author(s): John R. Casey, Michael J. Follows
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1004068

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
Cited by: 34
Author(s): Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming‐Sound Tsao, Igor Jurišica
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1004805

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cited by: 73
Author(s): Vaclav Cvicek, William A. Goddard, Ravinder Abrol
Software Mentions: 3
Published: over 10 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

10.1107/S0907444911056058

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in<i>BUSTER</i>
Cited by: 529
Author(s): Oliver S. Smart, Thomas Womack, Claus Flensburg, Peter M. Keller, W. A. Paciorek, A. Sharff, Clemens Vonrhein, G. Bricogne
Software Mentions: 3
Published: over 14 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

10.3390/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

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with <i>phenix.refine</i>
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 14 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: over 6 years ago

10.15252/msb.20209840

From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration
Cited by: 7
Author(s): Maria Palafox, Heta S Desai, Valerie A. Arboleda, Keriann M. Backus
Software Mentions: 3
Published: over 5 years ago

10.1107/S0907444910000272

Rapid chain tracing of polypeptide backbones in electron-density maps
Cited by: 5
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 years ago

10.1128/AEM.00808-18

Shuffling the Neutral Drift of Unspecific Peroxygenase in Saccharomyces cerevisiae
Cited by: 24
Author(s): Javier Martín-Díaz, Carmen Paret, Eva García-Ruiz, Patricia Molina‐Espeja, Miguel Alcalde
Software Mentions: 3
Published: about 8 years ago

10.1107/S0907444910029690

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from <i>Bacillus anthracis</i>
Cited by: 19
Author(s): Ekaterina Morgunova, Boris Illarionov, Sabine Saller, Aleksander Popov, Thota Sambaiah, Adelbert Bacher, Mary Cushman, Markus Fischer, Rudolf Ladenstein
Software Mentions: 3
Published: about 16 years ago

10.1093/ve/vev006

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
Cited by: 29
Author(s): Austin G. Meyer, Scott R. Spielman, Trevor Bedford, Claus O. Wilke
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pcbi.1004981

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
Cited by: 28
Author(s): Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1007892

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
Cited by: 2
Author(s): Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: almost 6 years ago

10.1074/mcp.RA120.002028

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
Cited by: 36
Author(s): Andreas Linden, Markus Deckers, Iwan Parfentev, Ralf Pflanz, Bettina Homberg, Piotr Neumann, Ralf Ficner, Peter Rehling, Henning Urlaub
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: over 12 years ago

10.3390/molecules26102929

Force Field Parameters for Fe2+4S2−4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies
Cited by: 1
Author(s): Maureen Bilinga Tendwa, Lorna J. Chebon, Kevin A. Lobb, Thommas M. Musyoka, Özlem Tastan Bishop
Software Mentions: 3
Published: over 5 years ago

10.1093/aobpla/plz075

Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava
Cited by: 8
Author(s): Ming-You Dong, Xian‐Wei Fan, Xiang-Yu Pang, Youzhi Li
Software Mentions: 3
Published: almost 7 years ago

10.1107/S1399004715005210

<i>In meso in situ</i> serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
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10.1074/mcp.RA119.001839

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
Cited by: 32
Author(s): Karl A.T. Makepeace, Yassene Mohammed, Elena L. Rudashevskaya, Evgeniy V. Petrotchenko, F.-Nora Vögtle, Chris Meisinger, Albert Sickmann, Christoph H. Borchers
Software Mentions: 3
Published: over 6 years ago

10.1016/j.molcel.2017.09.027

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants
Cited by: 54
Author(s): Mads Gabrielsen, Lori Buetow, Mark A. Nakasone, Syed Feroj Ahmed, Gary Sibbet, Brian O. Smith, Wei Zhang, Sachdev S. Sidhu, Danny T. Huang
Software Mentions: 3
Published: about 9 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

10.1016/j.molcel.2018.12.023

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex
Cited by: 67
Author(s): C.P. Hill, Vytautė Boreikaitė, Aman Kumar, Ana Casañal, Peter Kubík, Gianluca Degliesposti, Sarah Maslen, Angelica Mariani, Ottilie von Loeffelholz, Mathias Girbig, Mark Skehel, Lori A. Passmore
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0032858

Molecular and Antigenic Characterization of Reassortant H3N2 Viruses from Turkeys with a Unique Constellation of Pandemic H1N1 Internal Genes
Cited by: 17
Author(s): Yohannes Berhane, Helen Kehler, Katherine Handel, Tamiko Hisanaga, Wanhong Xu, Davor Ojkić, John Pasick
Software Mentions: 3
Published: over 14 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

10.1186/1471-2105-9-352

Alignment of protein structures in the presence of domain motions
Cited by: 48
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Software Mentions: 3
Published: about 18 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

10.1186/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

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 11 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

10.3390/md16100386

Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer’s Disease: A Computational Study
Cited by: 25
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Conxita Àvila, Melchor Sánchez-Martínez
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0140359

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions
Cited by: 20
Author(s): Andrea Bazzoli, Simon Kelow, John Karanicolas
Software Mentions: 3
Published: almost 11 years ago

10.3390/md18070349

Interactions of the α3β2 Nicotinic Acetylcholine Receptor Interfaces with α-Conotoxin LsIA and its Carboxylated C-terminus Analogue: Molecular Dynamics Simulations
Cited by: 3
Author(s): Jierong Wen, David J. Adams, Andrew Hung
Software Mentions: 3
Published: over 6 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

10.1186/1472-6807-6-4

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

10.1186/1471-2105-15-72

Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis
Cited by: 8
Author(s): Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Miriam Torres-Mendoza, M.E. Flores-Soto, Mildred Vázquez-Torres, Francisco Javier Gálvez-Gastélum, Arturo Viniegra‐Osorio, Marcelo Castillero-Manzano, Eduardo Vázquez-Valls
Software Mentions: 3
Published: over 12 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

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0140934

Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice
Cited by: 40
Author(s): Yue Chen, Xiaoman Wang, Li Zhou, Yi He, Dun Wang, Yanhua Qi, Dongxiang Jiang
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1008964

The evolution and functional divergence of the histone H2B family in plants
Cited by: 42
Author(s): Dazong Jiang, Michael Borg, Zdravko J. Lorković, Sean A. Montgomery, Akihisa Osakabe, Ramesh Yelagandula, Elin Axelsson, Frédéric Berger
Software Mentions: 3
Published: about 6 years ago

10.1007/s00412-019-00700-0

The molecular basis of monopolin recruitment to the kinetochore
Cited by: 15
Author(s): Rebecca Plowman, Namit Singh, Eelco C. Tromer, Angel Payan, Eris Duro, Christos Spanos, Juri Rappsilber, Berend Snel, Geert J.P.L. Kops, K.D. Corbett, Adèle L. Marston
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-68419-y

Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis
Cited by: 8
Author(s): Hye Lin Chun, So Yeon Lee, Sung Hoon Lee, Chang Sup Lee, Hyun Ho Park
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.03583

Structure and transport mechanism of the sodium/proton antiporter MjNhaP1
Cited by: 65
Author(s): Cristina Paulino, David Wöhlert, Ekaterina Kapotova, Özkan Yıldız, Werner Kühlbrandt
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-018-27051-7

The crystal structure of monoacylglycerol lipase from M. tuberculosis reveals the basis for specific inhibition
Cited by: 19
Author(s): P. Aschauer, R. Zimmermann, Rolf Breinbauer, Tea Pavkov‐Keller, Monika Oberer
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.4728

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from <i>Mycobacterium tuberculosis</i>
Cited by: 5
Author(s): Mingjing Yu, Chao Dou, Yijun Gu, Wei Cheng
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0116688

Identification of STAT1 and STAT3 Specific Inhibitors Using Comparative Virtual Screening and Docking Validation
Cited by: 29
Author(s): Małgorzata Szeląg, Anna Czerwoniec, Joanna Wesoły, Hans A.R. Bluyssen
Software Mentions: 3
Published: over 11 years ago