10.1098/rsob.160127

Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A
Cited by: 24
Author(s): Naoki Horikoshi, Yasuhiro Arimura, Hiroyuki Taguchi, Hitoshi Kurumizaka
Software Mentions: 2
Published: about 10 years ago

10.1098/rsob.160157

Exploring the active site of the <i>Streptococcus pneumoniae</i> topoisomerase IV–DNA cleavage complex with novel 7,8-bridged fluoroquinolones
Cited by: 18
Author(s): Ivan Laponogov, Xiao Su Pan, D. A. Veselkov, Ryan T. Cirz, Allan S. Wagman, Heinz Moser, L. Mark Fisher, Mark Sanderson
Software Mentions: 2
Published: almost 10 years ago

10.1098/rsob.160327

Structural and functional analysis of <i>Oceanobacillus iheyensis</i> macrodomain reveals a network of waters involved in substrate binding and catalysis
Cited by: 15
Author(s): Rubén Zapata-Pérez, F. Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Judith Juanhuix, Álvaro Sánchez‐Ferrer
Software Mentions: 2
Published: over 9 years ago

10.1098/rsob.170135

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, <i>Myodes glareolus</i>
Cited by: 6
Author(s): Grace M. Loxley, Jennifer Unsworth, Michael J. Turton, Alexandra Jebb, Kathryn S. Lilley, Deborah M. Simpson, Daniel J. Rigden, Jane L. Hurst, Robert J. Beynon
Software Mentions: 2
Published: almost 9 years ago

10.1042/BCJ20160806

<i>Neisseria meningitidis</i> factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy
Cited by: 18
Author(s): E. Malito, Paola Lo Surdo, Daniele Veggi, Laura Santini, Heather Stefek, Brunella Brunelli, Enrico Luzzi, Matthew J. Bottomley, Peter T. Beernink, María Scarselli
Software Mentions: 2
Published: over 9 years ago

10.3390/ph14030214

Evaluation of the Interactions between Human Serum Albumin (HSA) and Non-Steroidal Anti-Inflammatory (NSAIDs) Drugs by Multiwavelength Molecular Fluorescence, Structural and Computational Analysis
Cited by: 16
Author(s): Susana Amézqueta, José Luís Beltrán, Anna Maria Bolioli, Lluís Campos-Vicens, F. Javier Luque, Clara Ràfols
Software Mentions: 2
Published: over 5 years ago

10.1042/BCJ20200128

Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine
Cited by: 10
Author(s): Matthew J. Byrne, Nazia Nasir, Christine Basmadjian, Chitra Bhatia, Rory F. Cunnison, Katherine H. Carr, Corine Mas-Droux, Sharon Yeoh, Céline Cano, Richard Bayliss
Software Mentions: 2
Published: about 6 years ago

10.1107/S2059798320005355

Structural analysis of the PATZ1 BTB domain homodimer
Cited by: 4
Author(s): Sofia Piepoli, Aaron Alt, Canan Atılgan, Erika J. Mancini, Batu Erman
Software Mentions: 2
Published: about 6 years ago

10.3390/ph14070669

New (Iso)quinolinyl-pyridine-2,6-dicarboxamide G-Quadruplex Stabilizers. A Structure-Activity Relationship Study
Cited by: 7
Author(s): Enrico Cadoni, Pedro R. Magalhães, Rita M. Emídio, Eduarda Mendes, Jorge M. B. Vítor, Josué Carvalho, Carla Cruz, Bruno L. Victor, Alexandra Paulo
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jbc.2021.100771

Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP
Cited by: 11
Author(s): Avijit Dutta, Mona Batish, Vijay Parashar
Software Mentions: 2
Published: over 5 years ago

10.1107/S2059798317007021

High-resolution cryo-EM proteasome structures in drug development
Cited by: 10
Author(s): Edward P. Morris, Paula C. A. da Fonseca
Software Mentions: 2
Published: about 9 years ago

10.1042/BCJ20200507

Fragment-derived modulators of an industrial β-glucosidase
Cited by: 2
Author(s): Eleni Makraki, John F. Darby, Marta G. Carneiro, James D. Firth, Alex Heyam, Eiso Ab, Peter O’Brien, Gregg Siegal, Roderick E. Hubbard
Software Mentions: 2
Published: over 5 years ago

10.1016/j.jbc.2021.100823

Structures of the alkanesulfonate monooxygenase MsuD provide insight into C–S bond cleavage, substrate scope, and an unexpected role for the tetramer
Cited by: 5
Author(s): Jeremy Liew, Israa M. El Saudi, S. Nguyen, Denyce K. Wicht, Daniel Dowling
Software Mentions: 2
Published: about 5 years ago

10.1016/j.jbc.2021.100857

Oxalate decarboxylase uses electron hole hopping for catalysis
Cited by: 5
Author(s): Anthony J. Pastore, Ruijie D. Teo, Alvaro Montoya, M.J. Burg, Umar T. Twahir, Steven D. Bruner, David N. Beratan, Alexander Angerhofer
Software Mentions: 2
Published: about 5 years ago

10.1016/j.jbc.2021.100912

Cryo-EM reveals conformational flexibility in apo DNA polymerase ζ
Cited by: 4
Author(s): Chloe D. Truong, Theodore A. Craig, Gaofeng Cui, Maria Victoria Botuyan, Rachel A. Serkasevich, Kayi Y. Chan, Georges Mer, Po-Lin Chiu, Rajiv Kumar
Software Mentions: 2
Published: almost 5 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

10.1016/j.jbc.2021.100957

The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase
Cited by: 5
Author(s): Ankoor Patel, Jessica A.M. McBride, Brian L. Mark
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12915-021-01039-8

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors
Cited by: 30
Author(s): Yoshihisa Hirakawa, Masuo Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, M. Taira, Kazushi Kinbara, Toshiya Senda
Software Mentions: 2
Published: about 5 years ago

10.1186/s12915-015-0167-8

Role of electrostatic interactions for ligand recognition and specificity of peptide transporters
Cited by: 47
Author(s): Rajendra Boggavarapu, Jean-Marc Jeckelmann, Daniel Harder, Zöhre Ucurum, Dimitrios Fotiadis
Software Mentions: 2
Published: almost 11 years ago

10.3390/ph12020058

Insights into the Molecular Mechanisms of Eg5 Inhibition by (+)-Morelloflavone
Cited by: 11
Author(s): Tomisin Happy Ogunwa, Emiliano Laudadio, Roberta Galeazzi, Takayuki Miyanishi
Software Mentions: 2
Published: about 7 years ago

10.1016/j.jbc.2021.100995

Solution structures of human myeloma IgG3 antibody reveal extended Fab and Fc regions relative to the other IgG subclasses
Cited by: 8
Author(s): Valentina A. Spiteri, Margaret Goodall, James Doutch, Robert P. Rambo, Jayesh Gor, Stephen J. Perkins
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jbc.2021.101001

Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family
Cited by: 3
Author(s): Tatsuya Kondo, Miyu Kichijo, Akiho Maruta, Makoto Nakaya, Shigeo Takenaka, T. Arakawa, Shinya Fushinobu, Tatsuji Sakamoto
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jbc.2021.101031

Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability
Cited by: 1
Author(s): G. Dultz, Sanjay Kumar Srikakulam, Michael Konetschnik, Tetsuro Shimakami, Nadezhda T. Doncheva, Julia Dietz, Christoph Sarrazin, Ricardo M. Biondi, Stefan Zeuzem, Robert Tampé, Olga Kalinina, Christoph Welsch
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jbc.2021.101043

Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining
Cited by: 8
Author(s): Saiko Sugiura, Shogo Nakano, Masazumi Niwa, Fumihito Hasebe, Daisuke Matsui, Sohei Ito
Software Mentions: 2
Published: almost 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

10.1186/1741-7007-5-17

Ab initio modeling of small proteins by iterative TASSER simulations
Cited by: 459
Author(s): Sitao Wu, Jeffrey Skolnick, Yang Zhang
Software Mentions: 2
Published: about 19 years ago

10.1107/S2059798320000339

<i>SEQUENCE SLIDER</i>: expanding polyalanine fragments for phasing with multiple side-chain hypotheses
Cited by: 8
Author(s): Rafael J. Borges, Kathrin Meindl, Josep Triviño, Massimo Sammito, Ana María Medina, Claudia Millán, Martín Alcorlo, J.A. Hermoso, Marcos R.M. Fontes, Isabel Usón
Software Mentions: 2
Published: over 6 years ago

10.1186/s12915-017-0372-8

Ion- and water-binding sites inside an occluded hourglass pore of a trimeric intracellular cation (TRIC) channel
Cited by: 4
Author(s): Xiaomin Ou, Jing Guo, Long Wang, Hongxin Yang, Xiuying Liu, Jianyuan Sun, Zhongfan Liu
Software Mentions: 2
Published: about 9 years ago

10.1007/s00775-019-01639-4

Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine–valine ether cross-link formation in the R2-like ligand-binding oxidase
Cited by: 7
Author(s): Julia J. Griese, Ramona Kositzki, Michael Haumann, Martin Högbom
Software Mentions: 2
Published: over 7 years ago

10.3390/biom10050789

MARK4 Inhibited by AChE Inhibitors, Donepezil and Rivastigmine Tartrate: Insights into Alzheimer’s Disease Therapy
Cited by: 66
Author(s): Anas Shamsi, Saleha Anwar, Taj Mohammad, Mohamed F. Alajmi, Afzal Hussain, Tabish Rehman, Gulam Mustafa Hasan, Asimul Islam, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: about 6 years ago

10.3390/biom11081083

The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure
Cited by: 3
Author(s): Jessica Guillerm, Jean‐Marie Frère, Filip Meersman, André Matagne
Software Mentions: 2
Published: almost 5 years ago

10.1107/S1399004713030149

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex
Cited by: 29
Author(s): Jacob Lauwring Andersen, Tenna Juul Schrøder, Søren Christensen, Dorthe Strandbygård, Lone Tjener Pallesen, María García-Alai, Samsa Lindberg, Morten Langgård, Jørgen Eskildsen, Laurent David, Lena Tagmose, Klaus B. Simonsen, Philip Maltas, Lars Christian B. Rønn, Inge E.M. de Jong, Ibrahim Malik, Jan Egebjerg, Jens-Jacob Karlsson, U. Srinivas, Durga Rao Sakumudi, Pradheep Eradi, Steven P. Watson, Søren Thirup
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798315024110

Data-collection strategy for challenging native SAD phasing
Cited by: 40
Author(s): V. Oliéric, T. Weinert, Aaron D. Finke, Carolin Anders, Dianfan Li, Natacha Olieric, Camelia N. Borca, Michel O. Steinmetz, Martin Caffrey, Martin Jinek, Meitian Wang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0251067

Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism
Cited by: 4
Author(s): Sunghoon Kwon, Hye Lin Chun, Hyekyung Ha, So Yeon Lee, Hyun Ho Park
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0239702

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique
Cited by: 7
Author(s): Timothy R. Stachowski, M. Elizabeth Snell, Edward H. Snell
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0029406

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
Cited by: 21
Author(s): Melanie I. Stefan, David P. Marshall, Nicolas Le Novère
Software Mentions: 2
Published: over 14 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.pone.0231513

Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
Cited by: 8
Author(s): Keita Saito, Alexander Holm Viborg, Shiho Sakamoto, T. Arakawa, Chihaya Yamada, Kiyotaka Fujita, Shinya Fushinobu
Software Mentions: 2
Published: about 6 years ago

10.3390/pharmaceutics13081182

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses
Cited by: 12
Author(s): Dhanik Reshamwala, Sailee Shroff, Olivier Sheik Amamuddy, Valentino Laquintana, Nunzio Denora, Antonella Zacheo, Vili Lampinen, Vesa P. Hytönen, Özlem Tastan Bishop, Silke Krol, Varpu Marjomäki
Software Mentions: 2
Published: almost 5 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

10.1007/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

10.1107/S2059798319010866

Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
Cited by: 8
Author(s): C.D. Radka, Shaunivan Labiuk, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0187628

Plant-type phytoene desaturase: Functional evaluation of structural implications
Cited by: 25
Author(s): Julian Koschmieder, M. Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, Peter Beyer
Software Mentions: 2
Published: over 8 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

10.1371/journal.pone.0170260

Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host
Cited by: 5
Author(s): Konstantinos Koussis, Evi Goulielmaki, Anna Chalari, Chrislaine Withers‐Martinez, Inga Sidén‐Kiamos, Kai Matuschewski, Thanasis G. Loukeris
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0062021

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding
Cited by: 20
Author(s): R. Vinaik, Guennadi Kozlov, Kalle Gehring
Software Mentions: 2
Published: about 13 years ago

10.1107/S2059798320000212

3D domain swapping in the TIM barrel of the α subunit of<i>Streptococcus pneumoniae</i>tryptophan synthase
Cited by: 3
Author(s): K. Michalska, Marcin Kowiel, L. Bigelow, M. Endres, Mirosław Gilski, Mariusz Jaskólski, A. Joachimiak
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

10.1371/journal.pone.0128225

Structural and Biochemical Characterization of the Francisella tularensis Pathogenicity Regulator, Macrophage Locus Protein A (MglA)
Cited by: 8
Author(s): Bonnie J. Cuthbert, Richard G. Brennan, Maria A. Schumacher
Software Mentions: 2
Published: about 11 years ago

10.1107/S2059798318006356

Crystal structure of the spliceosomal DEAH-box ATPase Prp2
Cited by: 21
Author(s): Andreas Schmitt, Florian Hamann, Piotr Neumann, Ralf Ficner
Software Mentions: 2
Published: about 8 years ago

10.1186/1741-7007-9-48

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1
Cited by: 49
Author(s): Alexei Korennykh, Pascal F. Egea, А.A. Коростелев, J. Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, Peter Walter
Software Mentions: 2
Published: about 15 years ago

10.1186/s12915-017-0397-z

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues
Cited by: 93
Author(s): Rohan Bythell-Douglas, Carl J. Rothfels, Dennis Stevenson, Sean W. Graham, Gane Ka‐Shu Wong, David C. Nelson, Tom Bennett
Software Mentions: 2
Published: about 9 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

10.1007/s11120-017-0450-3

Crystal structure of Psb27 from Arabidopsis thaliana determined at a resolution of 1.85 Å
Cited by: 7
Author(s): Xingxing Cheng, Jiuyang Liu, Huan Zhang, Fudong Li, Zhang Shuya, Min Xu, Ke Ruan, Yuhua Wang, Aigen Fu
Software Mentions: 2
Published: over 8 years ago

10.1107/S1399004715002308

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array
Cited by: 67
Author(s): A.Y. Lyubimov, Thomas D. Murray, Antoine Koehl, Ismail Emre Araci, Monarin Uervirojnangkoorn, Oliver B. Zeldin, Aina E. Cohen, S. Michael Soltis, E.L. Baxter, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, James M. Berger
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0081753

Heterologous Expression of Mycobacterial Esx Complexes in Escherichia coli for Structural Studies Is Facilitated by the Use of Maltose Binding Protein Fusions
Cited by: 22
Author(s): M.A. Arbing, Sammy Chan, L.R. Harris, E. Kuo, T. Zhou, Christine J. Ahn, Ludivine David NGuyen, Cyndi Qixin He, Jamie Lu, Phuong T. Menchavez, Ae Sun Shin, Thomas Holton, M.R. Sawaya, Duilio Cascio, David Eisenberg
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0119760

In Silico Screening for Novel Inhibitors of DNA Polymerase III Alpha Subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)
Cited by: 14
Author(s): Alka Jadaun, Raja Sudhakar D, Naidu Subbarao, Aparna Dixit
Software Mentions: 2
Published: over 11 years ago

10.1186/s12915-017-0438-7

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook
Cited by: 7
Author(s): Clive S. Barker, Irina V. Meshcheryakova, Alla S. Kostyukova, Peter L. Freddolino, Fadel A. Samatey
Software Mentions: 2
Published: over 8 years ago

10.1111/pbi.12896

Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants
Cited by: 60
Author(s): Anna Bastet, Baptiste Lederer, Nathalie Giovinazzo, Xavier Arnoux, Sylvie German-Retana, Catherine Reinbold, Véronique Brault, Damien Garcia, Samia Djennane, Sophie Gersch, Olivier Lemaire, Christophe Robaglia, Jean‐Luc Gallois
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0206143

Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7
Cited by: 7
Author(s): Masoud Lotfan, Suman Choudhary, Munna Lal Yadav, Sudarshan Kumar, Surender Singh, Shveta Bathla, Preeti Rawat, Jai K. Kaushik, Ashok Kumar Mohanty
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0067536

Towards Ligand Docking Including Explicit Interface Water Molecules
Cited by: 58
Author(s): Gordon Lemmon, Jens Meiler
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0114903

An Integrative Computational Approach for Prioritization of Genomic Variants
Cited by: 7
Author(s): Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R. Paciorkowski, Ghayda Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al‐Gazali, Christopher E. Mason, M. Elizabeth Ross, Natalia Maltsev, T. Conrad Gilliam
Software Mentions: 2
Published: over 11 years ago

10.1107/S2059798318001365

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination
Cited by: 25
Author(s): Claudia Millán, Massimo Sammito, Airlie J. McCoy, Andrey Fabricio Ziem Nascimento, Giovanna Petrillo, Robert D. Oeffner, T. Dominguez-Gil, J.A. Hermoso, Randy J. Read, Isabel Usón
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0154046

Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics
Cited by: 2
Author(s): Gloria Ruiz-Gómez, John C. Hawkins, Patrick Jenny, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, M. Teresa Pisabarro
Software Mentions: 2
Published: about 10 years ago

10.1111/tpj.14409

Functional specialization of <scp>UDP</scp>‐glycosyltransferase 73P12 in licorice to produce a sweet triterpenoid saponin, glycyrrhizin
Cited by: 55
Author(s): Yuhta Nomura, Hikaru Seki, Tomonori Suzuki, Kiyoshi Ohyama, Masaharu Mizutani, Takashi Kaku, K Tamura, Eiichiro Ono, Manabu Horikawa, Hiroshi Sudo, Hiroaki Hayashi, Kazuki Saito, Toshiya Muranaka
Software Mentions: 2
Published: about 7 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

10.1242/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

10.1021/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

10.1186/1758-2946-4-17

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

10.1016/j.bpj.2021.01.012

Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Cited by: 49
Author(s): Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham Dokainish, Suyong Re, Yuji Sugita
Software Mentions: 2
Published: over 5 years ago

10.1186/2046-1682-5-7

Arbitrary protein−protein docking targets biologically relevant interfaces
Cited by: 37
Author(s): Juliette Martin, Richard Lavery
Software Mentions: 2
Published: about 14 years ago

10.1186/2046-1682-6-10

Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies
Cited by: 8
Author(s): Anke Steinbach, Christine K. Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W. Hartmann, Matthias Negri
Software Mentions: 2
Published: almost 13 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

10.1186/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

10.1016/j.bpj.2015.02.013

Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation
Cited by: 71
Author(s): Sonya M. Hanson, Simon Newstead, Kenton J. Swartz, Mark S.P. Sansom
Software Mentions: 2
Published: over 11 years ago

10.1016/j.bpj.2015.06.061

Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains
Cited by: 26
Author(s): James Krieger, İvet Bahar, Ingo H. Greger
Software Mentions: 2
Published: almost 11 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

10.1186/s13628-018-0048-y

Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments
Cited by: 6
Author(s): Aslı Yıldırım, Nathalie Brenner, Robert Sutherland, Michael Feig
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.0050297

Fabp7 Maps to a Quantitative Trait Locus for a Schizophrenia Endophenotype
Cited by: 176
Author(s): Akïharu Watanabe, Tomoko Toyota, Yuji Owada, Takeshi Hayashi, Yoshimi Iwayama, Miho Matsumata, Yuichi Ishitsuka, Akihiro Nakaya, Motoko Maekawa, Tetsuo Ohnishi, Ryoichi Arai, K. Sakurai, Kazuo Yamada, Hisatake Kondo, Kenji Hashimoto, Noriko Osumi, Takeo Yoshikawa
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pbio.1000589

Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases
Cited by: 86
Author(s): Vijay Parashar, Nicolas Mirouze, David Dubnau, Matthew B. Neiditch
Software Mentions: 2
Published: over 15 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

10.1002/jcc.26559

<scp> <i>MonteCarbo</i> </scp> : A software to generate and dock multifunctionalized ring molecules
Cited by: 0
Author(s): Santiago Alonso-Gil
Software Mentions: 2
Published: about 5 years ago

10.1107/S2059798317013043

Conformational dynamics of the essential sensor histidine kinase WalK
Cited by: 26
Author(s): Yongfei Cai, Mingyang Su, Ashfaq Ahmad, Xiaojie Hu, Jiayan Sang, Ling-Yuan Kong, Xingqiang Chen, Chen Wang, Jianwei Shuai, Aidong Han
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pbio.1002480

The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation
Cited by: 39
Author(s): Sohail Khoshnevis, Isabel Askenasy, Matthew C. Johnson, Maria D. Dattolo, Crystal L. Young-Erdos, M. Elizabeth Stroupe, Katrin Karbstein
Software Mentions: 2
Published: about 10 years ago

10.1007/s41048-018-0073-z

Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion
Cited by: 6
Author(s): Li Wang, Xian Chen, Xuzhen Guo, Jiasong Li, Qi Liu, Fuying Kang, Xudong Wang, Cheng Hu, Haiping Li, Weimin Gong, Wei Zhuang, Liu Xiao-hong, Jiangyun Wang
Software Mentions: 2
Published: almost 8 years ago

10.1210/js.2019-00260

Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1
Cited by: 14
Author(s): Richard Caswell, Martina Owens, Adam C. Gunning, Sian Ellard, Caroline F. Wright
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pbio.1001226

Structural Basis of Response Regulator Inhibition by a Bacterial Anti-Activator Protein
Cited by: 52
Author(s): Melinda D. Baker, Matthew B. Neiditch
Software Mentions: 2
Published: over 14 years ago

10.1186/1472-6750-11-85

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
Cited by: 36
Author(s): Gustavo R. Oliveira, Maria C. M. Silva, Wagner Alexandre Lucena, Erich Yukio Tempel Nakasu, Alexandre Augusto Pereira Firmino, Magda Aparecida Beneventi, Djair S.L. Souza, José Erick Galindo Gomes, José Dijair Antonino, Daniel J. Rigden, H. B. Ramos, Carlos Ricardo Soccol, Maria Fátima Grossi‐de‐Sá
Software Mentions: 2
Published: almost 15 years ago

10.1107/S1744309111019312

Conservation of a crystallographic interface suggests a role for β-sheet augmentation in influenza virus NS1 multifunctionality
Cited by: 9
Author(s): Philip S. Kerry, Eric C. Long, Margaret Taylor, Rosemary Russell
Software Mentions: 2
Published: almost 15 years ago

10.1107/S139900471402776X

Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove
Cited by: 24
Author(s): Marina E. Ivanova, Georgina Fletcher, Nicola O’Reilly, A. Purkiss, B. J. Thompson, Neil Q. McDonald
Software Mentions: 2
Published: over 11 years ago

10.1107/S2059798318018442

The atypical thiol–disulfide exchange protein α-DsbA2 from<i>Wolbachia pipientis</i>is a homotrimeric disulfide isomerase
Cited by: 4
Author(s): Patricia Walden, Andrew E. Whitten, Lakshmanane Premkumar, Maria A. Halili, Begoña Heras, G. J. King, Jennifer L. Martin
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20170001

Crystal structure of thermostable alkylsulfatase SdsAP from <i>Pseudomonas sp. S9</i>
Cited by: 3
Author(s): Lifang Sun, Pu Chen, Su Y, Zhixiong Cai, Lingwei Ruan, Xun Xu, Yunkun Wu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0021267

Expression of Enzymatically Inactive Wasp Venom Phospholipase A1 in Pichia pastoris
Cited by: 13
Author(s): Irina Borodina, Bettina M. Jensen, Tim Wagner, Maher Abou Hachem, Ib Søndergaard, Lars K. Poulsen
Software Mentions: 2
Published: about 15 years ago