10.1016/j.jmb.2010.01.035

Structural Basis of Substrate Binding in WsaF, a Rhamnosyltransferase from Geobacillus stearothermophilus
Cited by: 22
Author(s): Kerstin Steiner, Gregor Hagelueken, Paul Messner, Christina Schäffer, James H. Naismith
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-017-11508-2

Computational Cell Cycle Profiling of Cancer Cells for Prioritizing FDA-Approved Drugs with Repurposing Potential
Cited by: 25
Author(s): Yu‐Chen Lo, Silvia Senese, Bryan France, Ankur A. Gholkar, Robert Damoiseaux, Jorge Z. Torres
Software Mentions: 2
Published: almost 9 years ago

10.3390/biom10091239

N-Terminal Segment of TvCyP2 Cyclophilin from Trichomonas vaginalis Is Involved in Self-Association, Membrane Interaction, and Subcellular Localization
Cited by: 2
Author(s): Sarita Aryal, Heng-Ming Hsu, Yuan‐Chao Lou, Chien-Hsin Chu, Jung-Hsiang Tai, Chun‐Hua Hsu, Chinpan Chen
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes11060605

Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events
Cited by: 18
Author(s): Mohammed A. Rohaim, Rania F. El Naggar, Mohammed A. Abdelsabour, Mahmoud H. A. Mohamed, I. M. El-Sabagh, Muhammad Munir
Software Mentions: 2
Published: about 6 years ago

10.1016/j.jmb.2009.10.010

The Central Portion of Factor H (Modules 10–15) Is Compact and Contains a Structurally Deviant CCP Module
Cited by: 50
Author(s): Christoph Q. Schmidt, Andrew P. Herbert, Haydyn D. T. Mertens, Mara Guariento, Dinesh C. Soares, Dušan Uhrı́n, Arthur J. Rowe, Dmitri I. Svergun, Paul N. Barlow
Software Mentions: 2
Published: over 16 years ago

10.1186/1743-422X-10-269

Chikungunya virus capsid protein contains nuclear import and export signals
Cited by: 37
Author(s): Saijo Thomas, Jagdish Rai, Lijo John, Stephan Schaefer, Brigitte M. Pützer, Ottmar Herchenröder
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0082484

Structure-Based Analysis of A19D, a Variant of Transthyretin Involved in Familial Amyloid Cardiomyopathy
Cited by: 5
Author(s): Priscila S. Ferreira, Oliveira Sant’Anna, Nathalia Varejão, Cristina Ferreira Lima, Sérgio A. P. Novis, Renata V. Barbosa, Concy M. Caldeira, Franklin David Rumjanek, Salvador Ventura, Márcia Waddington Cruz, Débora Foguel
Software Mentions: 2
Published: over 12 years ago

10.1002/2211-5463.12931

High‐resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6
Cited by: 4
Author(s): Jonathan Davies, Amy Britton, Sai Man Liu, K. Ravi Acharya
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jmb.2011.03.047

Interaction of the p53 DNA-Binding Domain with Its N-Terminal Extension Modulates the Stability of the p53 Tetramer
Cited by: 79
Author(s): Eviatar Natan, Çetin Baloğlu, Kevin Pagel, Stefan Freund, Nina Morgner, Carol V. Robinson, Alan R. Fersht, A.C. Joerger
Software Mentions: 2
Published: about 15 years ago

10.1016/j.jmb.2009.07.026

Crystal Structures of Wzb of Escherichia coli and CpsB of Streptococcus pneumoniae, Representatives of Two Families of Tyrosine Phosphatases that Regulate Capsule Assembly
Cited by: 69
Author(s): Gregor Hagelueken, Hexian Huang, Iain L. Mainprize, Chris Whitfield, James H. Naismith
Software Mentions: 2
Published: almost 17 years ago

10.1002/2211-5463.12644

Structural insights into interactions between viral suppressor of <scp>RNA</scp> silencing protein p19 mutants and small <scp>RNA</scp>s
Cited by: 5
Author(s): Dana V. Foss, N.T. Schirle, Ian J. MacRae, John Paul Pezacki
Software Mentions: 2
Published: about 7 years ago

10.1002/2211-5463.12595

Molecular structure of a 5,10‐methylenetetrahydrofolate dehydrogenase from the silkworm <i>Bombyx mori</i>
Cited by: 4
Author(s): Mohammad Rashedul Haque, Akifumi Higashiura, Atsushi Nakagawa, Aiko Hirowatari, Shigeki Furuya, Kohji Yamamoto
Software Mentions: 2
Published: over 7 years ago

10.1016/j.jmb.2010.03.043

Solution Structure and Characterisation of the Human Pyruvate Dehydrogenase Complex Core Assembly
Cited by: 51
Author(s): Swetha Víjayakríshnan, Sharon M. Kelly, Robert J.C. Gilbert, Philip Callow, David Bhella, V. Trevor Forsyth, J. Gordon Lindsay, Olwyn Byron
Software Mentions: 2
Published: about 16 years ago

10.3390/genes12010122

A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity
Cited by: 9
Author(s): Mi Lu, Rolf Daniel
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0096809

Calponin-Like Chd64 Is Partly Disordered
Cited by: 10
Author(s): Małgorzata Kozłowska, Aneta Tarczewska, Michał Jakób, Kamil Szpotkowski, Magdalena Wojtas, Grzegorz Rymarczyk, Andrzej Ożyhar
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0092636

In-Silico Analysis of Binding Site Features and Substrate Selectivity in Plant Flavonoid-3-O Glycosyltransferases (F3GT) through Molecular Modeling, Docking and Dynamics Simulation Studies
Cited by: 12
Author(s): Ranu Sharma, Priyabrata Panigrahi, C.G. Suresh
Software Mentions: 2
Published: over 12 years ago

10.1007/s00109-019-01755-3

Molecular modeling of LDLR aids interpretation of genomic variants
Cited by: 8
Author(s): Eric W. Klee, Michael T. Zimmermann
Software Mentions: 2
Published: over 7 years ago

10.1007/s00894-016-2982-4

Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
Cited by: 17
Author(s): Tomasz Makarewicz, Rajmund Kaźmierkiewicz
Software Mentions: 2
Published: about 10 years ago

10.1007/s00894-012-1563-4

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain
Cited by: 94
Author(s): Antje Wolf, Karl N. Kirschner
Software Mentions: 2
Published: almost 14 years ago

10.1074/jbc.RA119.008610

Alternative folding to a monomer or homopolymer is a common feature of the type 1 pilus subunit FimA from enteroinvasive bacteria
Cited by: 7
Author(s): Dawid Zyla, A.E. Prota, Guido Capitani, Rudi Glockshuber
Software Mentions: 2
Published: about 7 years ago

10.1074/jbc.RA119.008817

A knottin scaffold directs the CXC-chemokine–binding specificity of tick evasins
Cited by: 21
Author(s): Angela Lee, Maud Déruaz, Christopher J. Lynch, Graham Davies, Khushboo Singh, Yara Alenazi, James R. O. Eaton, Akane Kawamura, Jeffrey P. Shaw, Amanda E. I. Proudfoot, João Marcos Domingues Dias, Shoumo Bhattacharya
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-14008-5

Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica
Cited by: 6
Author(s): Yen‐Yi Liu, Chih-Chieh Chen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12929-018-0444-2

CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population
Cited by: 10
Author(s): Alice Hálová, Jana Janoutová, Laura Ewerlingová, Vladimí­r Janout, Ondřej Bonczek, Tomáš Zeman, Tereza Gerguri, Vladimír J. Balcar, Omar Šerý
Software Mentions: 2
Published: about 8 years ago

10.1186/s12929-019-0589-7

Structural basis of polyethylene glycol recognition by antibody
Cited by: 27
Author(s): Cheng Chung Lee, Yu-Cheng Su, Tzu Ping Ko, Li-Hung Lin, Chih Ya Yang, Shu‐Wen Chang, Steve R. Roffler, Andrew H.‐J. Wang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1000923

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions
Cited by: 52
Author(s): Andreas Kowarsch, Angelika Fuchs, Dmitrij Frishman, Philipp Pagel
Software Mentions: 2
Published: almost 16 years ago

10.1186/1475-2875-13-313

Immunization against a merozoite sheddase promotes multiple invasion of red blood cells and attenuates Plasmodium infection in mice
Cited by: 3
Author(s): Ryan C. Smith, Daisy D. Colón-López, Jürgen Bosch
Software Mentions: 2
Published: almost 12 years ago

10.1007/s10858-015-9933-8

NMRFAM-SDF: a protein structure determination framework
Cited by: 4
Author(s): Hesam Dashti, Woonghee Lee, Marco Tonelli, Claudia C. Cornilescu, Gabriel Cornilescu, Fariba M. Assadi‐Porter, William M. Westler, Hamid R. Eghbalnia, John L. Markley
Software Mentions: 2
Published: about 11 years ago

10.1007/s10858-019-00247-3

Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations
Cited by: 4
Author(s): Songhwan Hwang, Carl Öster, Veniamin Chevelkov, Karin Giller, Adam Lange, Stefan Becker, Adam Lange
Software Mentions: 2
Published: about 7 years ago

10.1007/s10858-016-0029-x

Integrative NMR for biomolecular research
Cited by: 43
Author(s): Woonghee Lee, Gabriel Cornilescu, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, Samuel E. Butcher, Katherine Henzler‐Wildman, John L. Markley
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-019-55635-4

Damaging coding variants within kainate receptor channel genes are enriched in individuals with schizophrenia, autism and intellectual disabilities
Cited by: 10
Author(s): Maria Koromina, Miles Flitton, Alix Blockley, Ian R. Mellor, Helen Miranda Knight
Software Mentions: 2
Published: over 6 years ago

10.1007/s10858-021-00365-x

A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy
Cited by: 9
Author(s): A.L. Kantsadi, Emma Cattermole, Minos‐Timotheos Matsoukas, Georgios A. Spyroulias, Ioannis Vakonakis
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-56499-4

A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains
Cited by: 68
Author(s): Vivek Modi, Roland L. Dunbrack
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56458-z

Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers
Cited by: 7
Author(s): Tobias Schneider, Andrej Berg, Zeynel Ulusoy, Martin Gamerdinger, Christine Peter, Michael Kovermann
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56557-x

Structure-Guided Design of a Fluorescent Probe for the Visualization of FtsZ in Clinically Important Gram-Positive and Gram-Negative Bacterial Pathogens
Cited by: 20
Author(s): Edgar Ferrer-González, Junnosuke Fujita, Takumi Yoshizawa, Julia M. Nelson, Alyssa Pilch, Elani Hillman, M. Ozawa, Natsuko Kuroda, Hassan Al-Tameemi, Jeffrey M. Boyd, Edmond J. LaVoie, Hideki Matsumura, Daniel S. Pilch
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0191610

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii
Cited by: 1
Author(s): Bhumika S. Shah, Heather E. Ashwood, S.J. Harrop, Daniel N. Farrugia, Ian T. Paulsen, Bridget C. Mabbutt
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-56257-6

High resolution structural and functional analysis of a hemopexin motif protein from Dolichos
Cited by: 0
Author(s): Sarita Chandan Sharma, Ashish Kumar, Sharad Vashisht, Dinakar M. Salunke
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56135-1

Shortening injection matrix for serial crystallography
Cited by: 29
Author(s): Ki Hyun Nam
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56825-w

Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase
Cited by: 1
Author(s): Na Li, Ke Shi, Timsi Rao, Surajit Banerjee, Hideki Aihara
Software Mentions: 2
Published: over 6 years ago

10.1155/2016/8683713

Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans: An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle
Cited by: 1
Author(s): Sujay Ray, Arundhati Banerjee
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-020-57419-7

Conformational changes in Apolipoprotein N-acyltransferase (Lnt)
Cited by: 6
Author(s): B. Wiseman, Martin Högbom
Software Mentions: 2
Published: over 6 years ago

10.1016/j.chom.2020.06.010

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
Cited by: 280
Author(s): Jiandong Huo, Yuguang Zhao, Jingshan Ren, Daming Zhou, Duyvesteyn Hme., H. Ginn, L. Carrique, Tomas Malinauskas, R.R. Ruza, Pranav N.M. Shah, Tiong Kit Tan, Pramila Rijal, Naomi Coombes, Kevin R. Bewley, Julia A. Tree, Julika Radecke, Neil G. Paterson, Piyasa Supasa, Juthathip Mongkolsapaya, Gavin Screaton, Miles W. Carroll, Alain Townsend, Elizabeth E. Fry, Raymond J. Owens, D.I. Stuart
Software Mentions: 2
Published: almost 6 years ago

10.3390/molecules25071751

Arylaminopropanone Derivatives as Potential Cholinesterase Inhibitors: Synthesis, Docking Study and Biological Evaluation
Cited by: 3
Author(s): Anna Hudcová, Aleš Kroutil, Renata Kubínová, Adriana Garro, Lucas Gutiérrez, Ricardo D. Enriz, Michal Oravec, Jozef Csöllei
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-58316-9

Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha
Cited by: 7
Author(s): Natália Elisa Bernardes, C.A. Fukuda, Tainá D. da Silva, H.C. Oliveira, Andrea C. de Barros, Thiago R. Dreyer, Maria Célia Bertolini, Marcos R.M. Fontes
Software Mentions: 2
Published: over 6 years ago

10.34172/jcvtr.2020.02

Novel single nucleotide mutations in exon-10 of human coagulationFactor V gene in patients with pulmonary thromboembolism
Cited by: 1
Author(s): Latheef Kasala, D. Rajasekhar, V. Vanajakshamma
Software Mentions: 2
Published: over 6 years ago

10.1083/jcb.201910059

Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle
Cited by: 23
Author(s): Michela Serena, Ricardo Bastos, P.R. Elliott, Francis A. Barr
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.639489

Transcriptional Profiles of Genes Related to Stress and Immune Response in Rainbow Trout (Oncorhynchus mykiss) Symptomatically or Asymptomatically Infected With Vibrio anguillarum
Cited by: 8
Author(s): Zhi-Shuai Hou, Yuan-Ru Xin, Xiaodong Yang, Chu Zeng, Hong-Kui Zhao, Meng-Qun Liu, Mei-Zhao Zhang, Jeffrey G. Daniel, Jifang Li, Haishen Wen
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-59948-7

An endocannabinoid catabolic enzyme FAAH and its paralogs in an early land plant reveal evolutionary and functional relationship with eukaryotic orthologs
Cited by: 6
Author(s): Imdadul Haq, Aruna Kilaru
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.592447

Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism
Cited by: 4
Author(s): Xiaohui Wei, Song Wang, Zhuolin Li, Zibin Li, Zehui Qu, Suqiu Wang, Baohua Zou, Ruiying Liang, Chun Xia, Nianzhi Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.620494

Targeting the TLR2 Receptor With a Novel Thymopentin-Derived Peptide Modulates Immune Responses
Cited by: 4
Author(s): Wei Xin, Lulu Zhang, Rijun Zhang, Rujuan Wu, James N. Petitte, Yanfei Hou, Daoyuan Si, Baseer Ahmad, Henan Guo, Manyi Zhang, Qiang Cheng, Yucui Tong
Software Mentions: 2
Published: about 5 years ago

10.1111/jcmm.13547

Humanization of fibroblast growth factor 1 single‐chain antibody and validation for its antitumorigenic efficacy in breast cancer and glioma cells
Cited by: 11
Author(s): Xiaomin He, Shuyuan Du, Shiqian Gao, Jing‐Ying Chen, Ran‐Juan Cao, Zhenkai Xing, Alia Rizvi Syeda Kazim, Huali Yu, Qing‐Chuan Zheng, Xinen Zhu
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-60344-4

Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division
Cited by: 8
Author(s): A.W. Almawi, Laurence Langlois-Lemay, Stephen Boulton, Juan José Pulido González, Giuseppe Melacini, Damien D’Amours, Alba Guarné
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0046838

Fluorescence of Alexa Fluor Dye Tracks Protein Folding
Cited by: 25
Author(s): Simon Lindhoud, Adrie H. Westphal, Antonie J. W. G. Visser, Jan Willem Borst, C.P.M. van Mierlo
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1008099

LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena
Cited by: 24
Author(s): Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Gregory Minevich, Ewa Joachimiak, Dorota Włoga, Zheng Ruan, Natarajan Kannan, Stephen Bocarro, Anoosh Bahraini, Krishna Kumar Vasudevan, Karl‐Ferdinand Lechtreck, Eduardo Orias, Jacek Gaertig
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0154190

X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain
Cited by: 32
Author(s): Firas Fadel, Yuguang Zhao, A. Cousido-Siah, Francesc Xavier Ruiz, A. Mitschler, A. Podjarny
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1004533

The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in Caenorhabditis elegans
Cited by: 59
Author(s): Cristina Tocchini, J.J. Keusch, Sarah Miller, Susanne Finger, H. Gut, Michael Stadler, Rafal Ciosk
Software Mentions: 2
Published: almost 12 years ago

10.1007/s00018-019-03150-0

The PCNA interaction motifs revisited: thinking outside the PIP-box
Cited by: 69
Author(s): Andreas Prestel, Nanna Wichmann, João M. Martins, Riccardo Marabini, Noah Kassem, Sebastian S. Broendum, Marit Otterlei, Olaf Nielsen, Martin Willemoës, Michael Ploug, Wouter Boomsma
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2018.03102

Plumbagin Ameliorates Collagen-Induced Arthritis by Regulating Treg/Th17 Cell Imbalances and Suppressing Osteoclastogenesis
Cited by: 12
Author(s): Tingyu Wang, Han Qiao, Zanjing Zhai, Jun Zhang, Jianwei Tu, Xinyi Zheng, Nan Qian, Hong Zhou, Eryi Lu, Tingting Tang
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1009791

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation
Cited by: 7
Author(s): Carolina Alves Feliciano, B.E. Eckenroth, Oscar R. Diaz, Sylvie Doublié, Aimee Shen
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.662909

Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses
Cited by: 0
Author(s): Gwo-Yu Chuang, Chen‐Hsiang Shen, Catherine Cheung, Jason Gorman, Adrian Creanga, Michael Joyce, Kwanyee Leung, Reda Rawi, Lingshu Wang, Eun Sung Yang, Yongping Yang, Baoshan Zhang, Yi Zhang, Masaru Kanekiyo, Tongqing Zhou, Brandon J. DeKosky, Barney S. Graham, John R. Mascola, Peter D. Kwong
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2019.02698

In silico Design of an Epitope-Based Vaccine Ensemble for Chagas Disease
Cited by: 38
Author(s): Lucas Michel-Todó, Pedro A. Reche, Pascal Bigey, María Jesús Pinazo, Joaquím Gascón, Julio Alonso-Padilla
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1005569

LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice
Cited by: 20
Author(s): Krista A. Geister, Michelle L. Brinkmeier, Leonard Cheung, Jennifer Wendt, Melissa J. Oatley, Daniel L. Burgess, Kenneth M. Kozloff, James D. Cavalcoli, Sally A. Camper
Software Mentions: 2
Published: over 10 years ago

10.3389/fimmu.2020.01529

The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage
Cited by: 11
Author(s): Jeffrey Zhou, Hussain Zaidi, Therese Ton, Daniela Fera
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-61972-6

Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity
Cited by: 4
Author(s): Teruya Nakamura, Chie Hashikawa, Kohtaro Okabe, Yuya Yokote, Mami Chirifu, Sachiko Toma-Fukai, Narushi Nakamura, Mihoko Matsuo, Miho Kamikariya, Yoshinari Okamoto, Jin Gohda, Taishin Akiyama, Kentaro Semba, Shinji Ikemizu, Masami Otsuka, Jun Inoue, Yuriko Yamagata
Software Mentions: 2
Published: over 6 years ago

10.1007/s00018-019-03211-4

Discovering the chloride pathway in the CFTR channel
Cited by: 14
Author(s): Bianka Farkas, Hedvig Tordai, Rita Padányi, Attila Tordai, János Gera, Gábor Paragi, Tamás Hegedüs
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-62460-7

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor
Cited by: 7
Author(s): François Inizan, Myriam Hanna, Maxim Stolyarchuk, Isaure Chauvot de Beauchêne, Luba Tchertanov
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.621153

Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First
Cited by: 16
Author(s): Yanan Wu, Nianzhi Zhang, Keiichiro Hashimoto, Chun Xia, Johannes M. Dijkstra
Software Mentions: 2
Published: about 5 years ago

10.1242/jcs.226852

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing
Cited by: 36
Author(s): Tiina Viita, Salla Kyheröinen, Bina Prajapati, Jori Virtanen, Mikko J. Frilander, Markku Varjosalo, Maria K. Vartiainen
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-020-62548-0

Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily
Cited by: 9
Author(s): Paul Hoff Backe, Jon K. Laerdahl, Lene Svendsen Kittelsen, Bjørn Dalhus, Lars Mørkrid, Magnar Bjørås
Software Mentions: 2
Published: over 6 years ago

10.1242/jcs.258399

Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health
Cited by: 13
Author(s): Amber Knapp-Wilson, Gonçalo C. Pereira, Emma Buzzard, Holly C Ford, A. Richardson, Robin A. Corey, Chris Neal, Paul Verkade, Andrew P. Halestrap, Vicki A. M. Gold, Patricia E. Kuwabara, Ian Collinson
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-62759-5

First comprehensive TSC1/TSC2 mutational analysis in Mexican patients with Tuberous Sclerosis Complex reveals numerous novel pathogenic variants
Cited by: 14
Author(s): Miriam E. Reyna-Fabián, Nancy Leticia Hernández‐Martínez, Miguel Ángel Alcántara-Ortigoza, Jorge Tonatiuh Ayala-Sumuano, Sergio Enríquez-Flores, José A. Velázquez-Aragón, Alfredo Varela‐Echavarría, Carlos G. Todd-Quiñones, Ariadna González-del Ángel
Software Mentions: 2
Published: about 6 years ago

10.3390/molecules25194413

Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo
Cited by: 6
Author(s): Giovanny Aguilera-Durán, Antonio Romo-Mancillas
Software Mentions: 2
Published: almost 6 years ago

10.1021/acs.jctc.0c01281

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties
Cited by: 29
Author(s): Kara K. Grotz, Sergio Cruz-León, Nadine Schwierz
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules26082370

Promising Antidiabetic and Antimicrobial Agents Based on Fused Pyrimidine Derivatives: Molecular Modeling and Biological Evaluation with Histopathological Effect
Cited by: 20
Author(s): Fatma Bassyouni, Mohammad Tarek, Abeer Salama, Bassant M. M. Ibrahim, Sawsan Salah El Dine, Nemat A. Yassin, Amina Hassanein, Maysa E. Moharam, Mohamed Abdel‐Rehim
Software Mentions: 2
Published: about 5 years ago

10.1186/1758-2946-4-17

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Cited by: 5,518
Author(s): Marcus D. Hanwell, Donald Curtis, David Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey Hutchison
Software Mentions: 2
Published: almost 14 years ago

10.1038/s41598-020-65994-y

S92 phosphorylation induces structural changes in the N-terminus domain of human mitochondrial calcium uniporter
Cited by: 9
Author(s): Youngjin Lee, Jongseo Park, Gihwan Lee, Sanghwa Yoon, Choon Kee Min, Tae Kyun Kim, Toshiharu Yamamoto, Do Han Kim, Keun Woo Lee, Soo Hyun Eom
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-66480-1

Crystal structures of Uso1 membrane tether reveal an alternative conformation in the globular head domain
Cited by: 6
Author(s): Yoonyoung Heo, Hye‐Jin Yoon, Hyunjung Ko, Soonmin Jang, Hyung Ho Lee
Software Mentions: 2
Published: about 6 years ago

10.3390/molecules26092600

Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach
Cited by: 20
Author(s): Fábio G. Martins, André Melo, Sérgio F. Sousa
Software Mentions: 2
Published: about 5 years ago

10.1007/s11011-019-00465-6

Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA
Cited by: 20
Author(s): Himani Tanwar, Dileep Kumar, George Priya Doss C, Hatem Zayed
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.celrep.2021.109292

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Cited by: 343
Author(s): Bo Meng, Steven A Kemp, Guido Papa, Rawlings P. Datir, Isabella Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed A. Mohamed, Giulia Gallo, Nazia Thakur, Dami Collier, Petra Mlčochová, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. L. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra Gupta
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-65993-z

Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity
Cited by: 10
Author(s): Haydar Bulut, Shin-ichiro Hattori, Hiromi Aoki-Ogata, Hironori Hayashi, Debananda Das, Manabu Aoki, David A. Davis, Kalapala Venkateswara Rao, Prasanth R. Nyalapatla, Arun K. Ghosh, Hiroaki Mitsuya
Software Mentions: 2
Published: about 6 years ago

10.1016/j.celrep.2018.05.046

Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design
Cited by: 52
Author(s): Kimmo Rantalainen, Zachary T. Berndsen, Sasha Murrell, Liwei Cao, Oluwarotimi Omorodion, Jonathan L. Torres, Mengyu Wu, Jeffrey C. Umotoy, Jeffrey Copps, Pascal Poignard, Elise Landais, James C. Paulson, Ian A. Wilson, Andrew B. Ward
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.00760-20

Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses
Cited by: 76
Author(s): Yan‐Xi Tan, Theresa Schneider, Matthew Leong, L. Aravind, David Zhang
Software Mentions: 2
Published: about 6 years ago

10.1186/s13321-019-0390-3

Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening
Cited by: 5
Author(s): Anna Lovrics, Veronika F.S. Pape, Dániel Szisz, Adrián Kalászi, Petra Heffeter, Csaba Magyar, Gergely Szakács
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.01577-20

Beyond Toxin Transport: Novel Role of ABC Transporter for Enzymatic Machinery of Cereulide NRPS Assembly Line
Cited by: 10
Author(s): Agnieszka Gacek‐Matthews, Zuzana Chromiková, Michael Sulyok, Genia Lücking, Imrich Barák, Monika Ehling‐Schulz
Software Mentions: 2
Published: over 5 years ago

10.1186/s13321-020-00460-5

Molecular representations in AI-driven drug discovery: a review and practical guide
Cited by: 176
Author(s): Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist
Software Mentions: 2
Published: almost 6 years ago

10.3390/md15120366

Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer’s Disease Therapeutic Agents
Cited by: 39
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Melchor Sánchez-Martínez, Conxita Àvila
Software Mentions: 2
Published: over 8 years ago

10.1016/j.celrep.2019.01.073

Control of Bacterial Virulence through the Peptide Signature of the Habitat
Cited by: 39
Author(s): Emilia Krypotou, Mariela Scortti, C. Grundström, Melanie Oelker, Ben F. Luisi, A. Elisabeth Sauer‐Eriksson, José A. Vázquez‐Boland
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0033639

Evaluation of an Antimicrobial L-Amino Acid Oxidase and Peptide Derivatives from Bothropoides mattogrosensis Pitviper Venom
Cited by: 43
Author(s): Brunna Mary Okubo, Osmar N. Silva, Ludovico Migliolo, Diego G. Gomes, William F. Porto, Carla L. Batista, Carmel S. Ramos, Hortência H. S. Holanda, Simoni Campos Dias, Octávio L. Franco, Susana Elisa Moreno
Software Mentions: 2
Published: over 14 years ago

10.1172/JCI142823

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection
Cited by: 16
Author(s): Cory A. Brennick, Mariam M. George, Marmar Moussa, Adam T. Hagymasi, Sahar Al Seesi, Tatiana Shcheglova, Ryan P Englander, Grant L.J. Keller, Jeremy L. Balsbaugh, Brian M. Baker, Andrea Schietinger, Ion Măndoiu, Pramod K. Srivastava
Software Mentions: 2
Published: over 5 years ago

10.1016/j.celrep.2016.06.022

Structural Insights into Arl1-Mediated Targeting of the Arf-GEF BIG1 to the trans-Golgi
Cited by: 25
Author(s): Antonio Galindo, Nicolas Soler, Stephen H. McLaughlin, Myeong-Hee Yu, Roger L. Williams, Sean Munro
Software Mentions: 2
Published: about 10 years ago

10.1016/j.celrep.2018.09.087

Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth
Cited by: 89
Author(s): Kshitij Wagh, Edward F. Kreider, Yingying Li, Hannah J. Barbian, Gerald H. Learn, Elena E. Giorgi, Peter Hraber, Timothy Decker, Andrew G. Smith, Marcos Vinícius Pereira Gondim, Lindsey Gillis, Jamie M. Wandzilak, Gwo-Yu Chuang, Reda Rawi, Fangping Cai, Pierre Pellegrino, Ian Williams, Julie Overbaugh, Feng Gao, Peter D. Kwong, Barton F. Haynes, George M. Shaw, Persephone Borrow, Michael S. Seaman, Beatrice H. Hahn, Bette T. Korber
Software Mentions: 2
Published: almost 8 years ago

10.1128/mBio.02901-20

Transcriptional Silencing by TsrA in the Evolution of Pathogenic Vibrio cholerae Biotypes.
Cited by: 7
Author(s): Florence Caro, A. S. Rubin Jose, Nicole M. Place, John J. Mekalanos
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0200387

Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics
Cited by: 8
Author(s): Camilla Faoro, Lorna Wilkinson-White, Ann H. Kwan, Sandro F. Ataide
Software Mentions: 2
Published: almost 8 years ago

10.1007/s10822-020-00277-2

Conformational analysis of macrocycles: comparing general and specialized methods
Cited by: 16
Author(s): Gustav Olanders, Hiba Alogheli, Peter Brandt, Anders Karlén
Software Mentions: 2
Published: over 6 years ago

10.1007/s10822-020-00301-5

A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands
Cited by: 0
Author(s): Kamil Kuder, Ilona Michalik, Katarzyna Kieć‐Kononowicz, Peter Kolb
Software Mentions: 2
Published: over 6 years ago

10.1007/s10822-015-9839-2

Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding
Cited by: 8
Author(s): Barbara Kalinowska, Piotr Fabian, Katarzyna Stąpor, Irena Roterman
Software Mentions: 2
Published: over 11 years ago

10.1128/mBio.00452-21

Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion Export
Cited by: 15
Author(s): Mitchell A. Moseng, Meinan Lyu, Tanadet Pipatpolkai, Przemysław Glaza, Corey C. Emerson, Phoebe L. Stewart, Phillip J. Stansfeld, Edward Yu
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.02823-20

Molecular Basis for Bordetella pertussis Interference with Complement, Coagulation, Fibrinolytic, and Contact Activation Systems: the Cryo-EM Structure of the Vag8-C1 Inhibitor Complex
Cited by: 2
Author(s): Arun Dhillon, Justin C. Deme, Emily Furlong, Dorina Roem, Ilse Jongerius, Steven Ross Johnson, Susan M. Lea
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.01144-21

A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface
Cited by: 14
Author(s): K. McCarthy, Jiwon Lee, Akiko Watanabe, Masayuki Kuraoka, Lindsey R. Robinson-McCarthy, George Georgiou, Garnett Kelsoe, Stephen C. Harrison
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.01011-21

Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation
Cited by: 14
Author(s): Julia L. E. Willett, Jennifer L. Dale, Lucy M. Kwiatkowski, Jennifer Powers, Michelle L. Korir, Rhea Kohli, Aaron M. T. Barnes, Gary M. Dunny
Software Mentions: 2
Published: about 5 years ago