10.3390/ijms17040446

Structure of the PLP-Form of the Human Kynurenine Aminotransferase II in a Novel Spacegroup at 1.83 Å Resolution
Cited by: 13
Author(s): Alireza Nematollahi, Guorong Sun, S.J. Harrop, Jane R. Hanrahan, W. Bret Church
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0235133

Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme
Cited by: 1
Author(s): Eyong Egbe, Colin Levy, Lydia Tabernero
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0056742

Towards Improved Quality of GPCR Models by Usage of Multiple Templates and Profile-Profile Comparison
Cited by: 50
Author(s): Dorota Latek, Paweł Pasznik, Teresa Carlomagno, Sławomir Filipek
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0134084

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
Cited by: 12
Author(s): Radhika Ganu, Yasuko Ishida, Markos Koutmos, Sergios‐Orestis Kolokotronis, Alfred L. Roca, Timothy A. Garrow, Lawrence B. Schook
Software Mentions: 2
Published: over 10 years ago

10.1038/srep45505

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2
Cited by: 29
Author(s): Kaifa Wei, Yuhan Li
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms17122116

Discovery of a New Class of Cathepsin K Inhibitors in Rhizoma Drynariae as Potential Candidates for the Treatment of Osteoporosis
Cited by: 17
Author(s): Zuo-Cheng Qiu, Xiaoli Dong, Yi Dai, Gao Keng Xiao, Xin Luan Wang, Ka-Chun Wong, Man Sau Wong, Xin Yao
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0026251

Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding
Cited by: 28
Author(s): Sushmita Kaushik, Ramanathan Sowdhamini
Software Mentions: 2
Published: almost 14 years ago

10.1038/srep08560

The catalytic role of the M2 metal ion in PP2Cα
Cited by: 16
Author(s): Chang Pan, Junyi Tang, Yaping Xu, Xiao Peng, Hongda Liu, Hao-an Wang, Wenbo Wang, Fanyue Meng, Xiao Yu, Junying Sun
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-00147-2

PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3
Cited by: 41
Author(s): Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
Software Mentions: 2
Published: over 8 years ago

10.3389/fmolb.2021.658906

Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl
Cited by: 5
Author(s): Tülay Karakulak, Ahmet Süreyya Rifaioğlu, João P. G. L. M. Rodrigues, Ezgi Karaca
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0063370

Structural Basis for the Oligomerization-State Switch from a Dimer to a Trimer of an Engineered Cortexillin-1 Coiled-Coil Variant
Cited by: 2
Author(s): Saša Bjelić, Mara M. Wieser, Daniel Frey, Christian U. Stirnimann, Mark R. Chance, Rolf Jaussi, Michel O. Steinmetz, Richard A. Kammerer
Software Mentions: 2
Published: over 12 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: about 5 years ago

10.1038/s41598-017-01186-5

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine
Cited by: 12
Author(s): Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, А.A. Коростелев
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms18071336

Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin
Cited by: 9
Author(s): Ashwani Sharma, Gonzalo Sáez-Calvo, Natacha Olieric, Francisco de Asís Balaguer, Isabel Barasoaín, Clemens Lamberth, J. Fernando Díaz, Michel O. Steinmetz
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-00917-y

A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Cited by: 21
Author(s): Shigetoshi Oiki, Bunzo Mikami, Yukie Maruyama, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0193028

Folic acid derived-P5779 mimetics regulate DAMP-mediated inflammation through disruption of HMGB1:TLR4:MD-2 axes
Cited by: 13
Author(s): Shan Sun, Mingzhu He, Yongjun Wang, Huan Yang, Yousef Al‐Abed
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0091232

Molecular Recognition of the Neurotransmitter Acetylcholine by an Acetylcholine Binding Protein Reveals Determinants of Binding to Nicotinic Acetylcholine Receptors
Cited by: 34
Author(s): Jeppe Olsen, Thomas Balle, Michael Gajhede, Philip K. Ahring, J.S. Kastrup
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-017-01057-z

Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis
Cited by: 22
Author(s): Stefano Donini, Davide M. Ferraris, Riccardo Miggiano, Alberto Massarotti, Menico Rizzi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0075446

A Purine Analog Synergizes with Chloroquine (CQ) by Targeting Plasmodium falciparum Hsp90 (PfHsp90)
Cited by: 23
Author(s): Dea Shahinas, Asongna Folefoc, Tony Taldone, Gabriela Chiosis, Ian Crandall, Dylan R. Pillai
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-017-01989-6

Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae
Cited by: 8
Author(s): Min Xu, Yizhi Wang, Xiu‐An Yang, Tao Jiang, Wei Xie
Software Mentions: 2
Published: over 8 years ago

10.3390/molecules25122884

Imunofan—RDKVYR Peptide—Stimulates Skin Cell Proliferation and Promotes Tissue Repair
Cited by: 6
Author(s): Justyna Sawicka, Maria Dzierżyńska, Anna Wardowska, Milena Deptuła, Piotr Rogujski, Paweł Sosnowski, Natalia Filipowicz, Alina Mieczkowska, Piotr Sass, Anna Pawlik, Aleksandra Hać, Adriana Schumacher, Magdalena Gucwa, Natalia Karska, Jolanta Kamińska, Rafał Płatek, Jarosław Mazuryk, Jacek Zieliński, Karolina Kondej, Piotr Młynarz, Piotr Mucha, Piotr Skowron, Łukasz Janus, Anna Herman-Antosiewicz, Paweł Sachadyn, Artur Czupryn, Arkadiusz Piotrowski, Michał Pikuła, Sylwia Rodziewicz‐Motowidło
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0123195

An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2) Selective Agonist
Cited by: 12
Author(s): Nadendla EswarKumar, Catherine Teyssier, V. Delfosse, Valérie Vivat, Krishnasamy Gunasekaran, Hinrich Gronemeyer, William Bourguet, Pierre Germain
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms19010224

Genome-Wide Identification, Expression, and Functional Analysis of the Alkaline/Neutral Invertase Gene Family in Pepper
Cited by: 23
Author(s): Long-Bin Shen, Yuan Yao, He Huang, Yuling Qin, Ziji Liu, Liu Weixia, Zhiqiang Qi, Yang Liu, Zhen-Mu Cao, Yan Yang
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-02823-9

Efficient Generation of Bispecific Murine Antibodies for Pre-Clinical Investigations in Syngeneic Rodent Models
Cited by: 31
Author(s): Aran F. Labrijn, Joyce Meesters, Matthew W. Bunce, Anthony A. Armstrong, Sandeep Somani, Tom Nesspor, Mark L. Chiu, Işıl Altıntaş, Sandra Verploegen, Janine Schuurman, Paul W.H.I. Parren
Software Mentions: 2
Published: over 8 years ago

10.3389/fchem.2018.00437

Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae
Cited by: 18
Author(s): Jianxun Zhu, Yang Li, Jinzhi Wang, Zeyang Yu, Ye Liu, Yi Tong, Wei Han
Software Mentions: 2
Published: about 7 years ago

10.3389/fchem.2021.735768

Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain
Cited by: 3
Author(s): Seema A. Kulkarni, Sabari B.B. Krishnan, Bavya Chandrasekhar, Kaushani Banerjee, Honglae Sohn, Thirumurthy Madhavan
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-02805-x

A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases
Cited by: 32
Author(s): Rubén M. Buey, David Fernández‐Justel, Íñigo Marcos‐Alcalde, Graeme Winter, Paulino Gómez‐Puertas, José M. de Pereda, José Luis Revuelta
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-02803-z

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method
Cited by: 22
Author(s): Suk-Jun Youn, Nayoung Kwon, Ji Hyun Lee, Jin Hong Kim, Jin‐Woo Choi, Hayyoung Lee, Jie‐Oh Lee
Software Mentions: 2
Published: over 8 years ago

10.3389/fchem.2017.00051

Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis
Cited by: 19
Author(s): Linda Oyama, Jean-Adrien Crochet, Joan E. Edwards, Susan Elizabeth Girdwood, Alan Cookson, Narcís Fernández-Fuentes, Kai Hilpert, Peter N. Golyshin, Olga V. Golyshina, Florence Privé, Matthias Hess, Hilário Cuquetto Mantovani, Christopher J. Creevey, Sharon Huws
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-03220-y

Bacterial protease uses distinct thermodynamic signatures for substrate recognition
Cited by: 13
Author(s): G.A. Bezerra, Yuko Ohara‐Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José Antonio Márquez, Takayuki Nemoto, Kristina Djinović-Carugo
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0234869

Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018
Cited by: 7
Author(s): Xiaonan Zhao, Han-Ju Zhang, Duo Li, Ji Zhou, Y. Chen, Yanhong Sun, Adeniyi C. Adeola, Xiaoqing Fu, Yong Shao, Meiling Zhang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22147288

Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain
Cited by: 1
Author(s): Francisco Andrés Peralta, J. Pablo Huidobro‐Toro, Raúl Mera‐Adasme
Software Mentions: 2
Published: over 4 years ago

10.3390/genes12091345

Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters
Cited by: 3
Author(s): François Boudsocq, Maya Salhi, Sophie Barbe, Jean‐Yves Bouet
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0085940

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site
Cited by: 47
Author(s): Young Do Kwon, Judith M. LaLonde, Yongping Yang, Mark A. Elban, Akihiro Sugawara, Joel R. Courter, David M. Jones, Amos B. Smith, Asim K. Debnath, Peter D. Kwong
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms22147341

Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
Cited by: 5
Author(s): Mateusz Kurciński, Sebastian Kmiecik, M. Zalewski, Andrzej Koliński
Software Mentions: 2
Published: over 4 years ago

10.1186/s13071-017-2523-8

Multidrug resistance-associated protein 4 is a bile transporter of Clonorchis sinensis simulated by in silico docking
Cited by: 7
Author(s): Fuhong Dai, Won Gi Yoo, Ji Yun Lee, Yao Lu, Jhang Ho Pak, Woon-Mok Sohn, Sung-Jong Hong
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-03664-2

Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis
Cited by: 48
Author(s): Na Yang, Xuehui Liu, Da Teng, Zhanzhan Li, Xiumin Wang, Ruoyu Mao, Xiao Wang, Ya Hao, Jianhua Wang
Software Mentions: 2
Published: over 8 years ago

10.3389/fchem.2021.640994

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations
Cited by: 5
Author(s): Congcong Li, Siao Chen, Tianci Huang, Fangning Zhang, Jiawei Yuan, Hao Teng Chang, Wannan Li, Wei Han
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22157934

Simulations of Promising Indolizidine—α6-β2 Nicotinic Acetylcholine Receptor Complexes
Cited by: 1
Author(s): Francis A. Acquah, Matthew Paramel, Adama Kuta, Syed R. Hussaini, David R. Wallace, Blaine H. M. Mooers
Software Mentions: 2
Published: over 4 years ago

10.3389/fchem.2020.619470

Membrane Protein Structures in Lipid Bilayers; Small-Angle Neutron Scattering With Contrast-Matched Bicontinuous Cubic Phases
Cited by: 4
Author(s): Charlotte E. Conn, Liliana de Campo, Andrew E. Whitten, Christopher J. Garvey, Anwen M. Krause‐Heuer, Leonie van ’t Hag
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41435-020-00120-6

Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity
Cited by: 35
Author(s): Irfan Hussain, Nashaiman Pervaiz, Abbas Khan, Shoaib Saleem, Huma Shireen, Dong‐Qing Wei, Viviane Labrie, Yīmíng Bào, Amir Ali Abbasi
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41436-021-01134-9

Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation
Cited by: 8
Author(s): Andrea D. Thompson, Adam S. Helms, Anamika Kannan, Jaime Yob, Neal K. Lakdawala, Samuel G. Wittekind, Alexandre C. Pereira, Daniel Jacoby, Steven D. Colan, Euan A. Ashley, Sara Saberi, James S. Ware, Jodie Ingles, Christopher Semsarian, Michelle Michels, Francesco Mazzarotto, Iacopo Olivotto, Carolyn Y. Ho, Sharlene M. Day
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22168581

Targeting Lipocalin-2 in Inflammatory Breast Cancer Cells with Small Interference RNA and Small Molecule Inhibitors
Cited by: 8
Author(s): Ginette S Santiago-Sánchez, Ricardo Noriega-Rivera, Eliud Hernandez O'Farril, Fatma Valiyeva, Blanca I Quiñones-Díaz, Emilly Schlee Villodre, Bisrat G. Debeb, Andrea Rosado-Albacarys, Pablo E. Vivas‐Mejía
Software Mentions: 2
Published: over 4 years ago

10.3390/biom10040615

Insight into the RssB-Mediated Recognition and Delivery of σs to the AAA+ Protease, ClpXP
Cited by: 10
Author(s): Dimce Micevski, Kornelius Zeth, Terrence D. Mulhern, Verena J. Schuenemann, Jessica E. Zammit, Kaye N. Truscott, David A. Dougan
Software Mentions: 2
Published: over 5 years ago

10.1590/1678-4685-GMB-2020-0393

Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing
Cited by: 1
Author(s): Natália Duarte Linhares, P. Wilk, E. Wator, Meire A. Tostes, M.S. Weiss, Sérgio D.J. Pena
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22179140

Structural and Functional Characterizations of Cancer Targeting Nanoparticles Based on Hepatitis B Virus Capsid
Cited by: 0
Author(s): Yunseok Heo, Hyomin Jeong, Youngki Yoo, Ji-Hye Yun, Bumhan Ryu, Young-je Cha, Boram Lee, Ye-Eun Jeon, Jongmin Kim, S.-H. Jeong, Eunji Jo, Jae Sung Woo, Jeewon Lee, Hyun-Soo Cho, Weontae Lee
Software Mentions: 2
Published: about 4 years ago

10.3389/fchem.2018.00650

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering
Cited by: 30
Author(s): Sérgio M. Marques, David Bednář, Jiřı́ Damborský
Software Mentions: 2
Published: almost 7 years ago

10.1017/S0016672319000065

In trans variant calling reveals enrichment for compound heterozygous variants in genes involved in neuronal development and growth.
Cited by: 2
Author(s): Allison Cox, Fillan Grady, Gabriel Vélez, Vinit B. Mahajan, Polly J. Ferguson, Andrew Kitchen, Benjamin W. Darbro, Alexander G. Bassuk
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms22189771

Insights into Comparative Modeling of VHH Domains
Cited by: 3
Author(s): Akhila Melarkode Vattekatte, Fréderic Cadet, Jean‐Christophe Gelly, Alexandre G. de Brevern
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-05234-y

Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases
Cited by: 2
Author(s): Abhishek Jamwal, Manickam Yogavel, M. Z. Abdin, Swatantra Kumar Jain, Amit Sharma
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-05509-4

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
Cited by: 69
Author(s): Min Fey Chek, Sunyong Kim, Tomoyuki Mori, Hasni Arsad, Mohammed Razip Samian, Kumar Sudesh, Toshio Hakoshima
Software Mentions: 2
Published: over 8 years ago

10.3390/v12080812

Structural and Biological Basis of Alphacoronavirus nsp1 Associated with Host Proliferation and Immune Evasion
Cited by: 17
Author(s): Zhou Shen, Yiling Yang, Siqi Yang, Guangxu Zhang, Shaobo Xiao, Zhen F. Fu, Guiqing Peng
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2008-9-8-r121

Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules
Cited by: 86
Author(s): Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult, Joel L. Sussman
Software Mentions: 2
Published: almost 18 years ago

10.3390/ijms221810022

The CXC Chemokine Receptors in Four-Eyed Sleeper (Bostrychus sinensis) and Their Involvement in Responding to Skin Injury
Cited by: 3
Author(s): Meng-Dan Dong, Hong Zhang, Chengyu Mo, Wenjing Li, Wanwan Zhang, Kuntong Jia, Wei Liu, Meisheng Yi
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-05657-7

Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI)
Cited by: 4
Author(s): Sebastián Esperante, Giovanni Covaleda, Sebastián A. Trejo, Sílvia Bronsoms, Francesc X. Aviles, Salvador Ventura
Software Mentions: 2
Published: over 8 years ago

10.3390/molecules24010142

Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays
Cited by: 19
Author(s): Magambo Phillip Kimuda, Dustin Laming, Özlem Tastan Bishop
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms221910640

Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM
Cited by: 10
Author(s): Miha Pavšič
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-05627-z

X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid
Cited by: 12
Author(s): Christian Lizak, L.J. Worrall, Lars Baumann, Moritz M. Pfleiderer, Gesa Volkers, Tianjun Sun, Lyann Sim, Warren W. Wakarchuk, Stephen G. Withers, N.C.J. Strynadka
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0170232

NOD1CARD Might Be Using Multiple Interfaces for RIP2-Mediated CARD-CARD Interaction: Insights from Molecular Dynamics Simulation
Cited by: 15
Author(s): Jitendra Maharana, Sukanta Kumar Pradhan, Sachinandan De
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms221910862

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis
Cited by: 7
Author(s): Carolina Rodrigues, Patrícia T. Borges, Magalí F. Scocozza, Diogo Silva, André Taborda, Vânia Brissos, Carlos Frazão, Lı́gia O. Martins
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms221910821

Prediction Models for Agonists and Antagonists of Molecular Initiation Events for Toxicity Pathways Using an Improved Deep-Learning-Based Quantitative Structure–Activity Relationship System
Cited by: 6
Author(s): Yasunari Matsuzaka, Shin Totoki, Kentaro Handa, Tetsuyoshi Shiota, Kota Kurosaki, Yoshihiro Uesawa
Software Mentions: 2
Published: about 4 years ago

10.3389/fendo.2018.00657

Metformin Is a Direct SIRT1-Activating Compound: Computational Modeling and Experimental Validation
Cited by: 82
Author(s): Elisabet Cuyàs, Sara Verdura, Laura Llorach-Parés, Salvador Fernández-Arroyo, Jorge Joven, Begoña Martin‐Castillo, Joaquim Bosch-Barrera, Joan Brunet, Alfons Nonell-Canals, Melchor Sánchez-Martínez, Javier A. Menendez
Software Mentions: 2
Published: about 7 years ago

10.1186/s12951-019-0512-0

Design and site-directed compartmentalization of gold nanoclusters within the intrasubunit interfaces of ferritin nanocage
Cited by: 16
Author(s): Jiachen Zang, Bowen Zheng, Xiuqing Zhang, Paolo Arosio, Guanghua Zhao
Software Mentions: 2
Published: over 6 years ago

10.1186/s12974-018-1060-5

Benefits of VCE-003.2, a cannabigerol quinone derivative, against inflammation-driven neuronal deterioration in experimental Parkinson’s disease: possible involvement of different binding sites at the PPARγ receptor
Cited by: 45
Author(s): Concepción Garcı́a, María Gómez‐Cañas, Sonia Burgaz, Belén Palomares, Yolanda Gómez‐Gálvez, Cristina Palomo-Garo, Sara Campo, Joel Ferrer-Hernández, Carolina Pavicic, Carmen Navarrete, M. Luz Bellido, Moisés Garcı́a-Arencibia, M. Ruth Pazos, Eduardo Muñóz, Javier Fernández‐Ruiz
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-05268-2

Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber
Cited by: 25
Author(s): Lorena Ilcu, Wolf Röther, Jakob Birke, Anton Brausemann, Oliver Einsle, Dieter Jendrossek
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-06612-2

Evaluation of Sofosbuvir (β-D-2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine) as an inhibitor of Dengue virus replication #
Cited by: 51
Author(s): Hongtao Xu, Susan P. Colby-Germinario, Said Hassounah, Clare Fogarty, Nathan Osman, Navaneethan Palanisamy, Ying-Shan Han, Maureen Oliveira, Yudong Quan, Mark A. Wainberg
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-06023-3

Search for non-lactam inhibitors of mtb β-lactamase led to its open shape in apo state: new concept for antibiotic design
Cited by: 10
Author(s): Amin Sagar, Nazia Haleem, Yaawar Mir Bashir, . Ashish
Software Mentions: 2
Published: over 8 years ago

10.1155/2021/6670834

High Expression of Interleukin-2 Receptor Subunit Gamma Reveals Poor Prognosis in Human Gastric Cancer
Cited by: 2
Author(s): Deping Wang, Rong Zhao, Yuehong Qi, Jing Shen, Jiayi Hou, Mei-Yue Wang, Xiaogang Bi, Xiaoqing Guo, Ji‐Min Cao
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-017-05594-5

Escape from humoral immunity is associated with treatment failure in HIV-1-infected patients receiving long-term antiretroviral therapy
Cited by: 6
Author(s): Yabo Ouyang, Qianqian Yin, Wei Li, Zhenpeng Li, Desheng Kong, Yanling Wu, Kui Hong, Hui Xing, Yiming Shao, Shibo Jiang, Tianlei Ying, Liying Ma
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-06278-w

Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF
Cited by: 11
Author(s): Christina Diederich, Mario Leypold, Martin Culka, Hansjörg Weber, Rolf Breinbauer, G. Matthias Ullmann, Wulf Blankenfeldt
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-06578-1

Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site
Cited by: 11
Author(s): Shivendra Pratap, Aditya Dev, Vijay Kumar, Ravi Yadav, M. Narwal, Shailly Tomar, Pravindra Kumar
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-01705-4

Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis
Cited by: 16
Author(s): Yunrong Gao, Defeng Li, Joy Fleming, Ya‐Feng Zhou, Ying Liu, Jiao-Yu Deng, Lin Zhou, Jie Zhou, Guofeng Zhu, Xian-En Zhang, Dacheng Wang, Lijun Bi
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-06575-4

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene
Cited by: 70
Author(s): Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Kumar Yadav, A. Krokhotin, Nikolay V. Dokholyan
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.8612

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress
Cited by: 57
Author(s): Seajin Oh, Ryan A. Flynn, Stephen N. Floor, James Purzner, Lance Martin, T. Brian, Simone Schubert, Dedeepya Vaka, A. Sorana Morrissy, Yisu Li, Marcel Kool, Volker Hovestadt, David Jones, Paul A. Northcott, Thomas S. Risch, Hans Jörg Warnatz, Marie Laure Yaspo, Christopher M. Adams, Ryan D. Leib, Marcus R. Breese, Marco A. Marra, David Malkin, Peter Lichter, Jennifer A. Doudna, Stefan M. Pfister, Michael D. Taylor, Howard Y. Chang, Yoon Jae Cho
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-06446-y

A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters
Cited by: 27
Author(s): Jonai Pujol‐Giménez, Matthias A. Hediger, Gergely Gyimesi
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-07436-w

Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus
Cited by: 57
Author(s): Varahalarao Vadlapudi, Nabajyoti Borah, Kanaka Raju Yellusani, Sriramya Gade, P. Sunder Ram Reddy, Maheshwari Rajamanikyam, Lakshmi Vempati, Satya Prakash Gubbala, Pankaj Chopra, Suryanarayana Murty Upadhyayula, Ramars Amanchy
Software Mentions: 2
Published: over 8 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: about 5 years ago

10.1371/journal.pone.0015199

Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution
Cited by: 92
Author(s): Tom Martin, Shunwen Lu, Herman van Tilbeurgh, Daniel R. Ripoll, Christina Dixelius, B. Gillian Turgeon, Robert Debuchy
Software Mentions: 2
Published: almost 15 years ago

10.18632/oncotarget.10599

<i>In silico</i>predicted structural and functional insights of all missense mutations on 2B domain of<i>K1/K10</i>causing genodermatoses
Cited by: 5
Author(s): Santasree Banerjee, Qian Wu, Yuyi Ying, Yanni Li, Matsuyuki Shirota, Dante Neculai, Chen Li
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0128310

Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor
Cited by: 15
Author(s): Peter K. Quashie, Ying-Shan Han, Said Hassounah, Thibault Mésplède, Mark A. Wainberg
Software Mentions: 2
Published: over 10 years ago

10.1093/gbe/evz266

Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates
Cited by: 64
Author(s): Guangshuai Liu, Huanxin Zhang, Chao Zhao, Honghai Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-08303-4

Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners
Cited by: 12
Author(s): Jakub Gemperle, R. Hexnerova, Martin Lepšı́k, Petr Těšina, Michal Dibus, Marián Novotný, Jan Brábek, Václav Veverka, Daniel Rösel
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-08834-w

Structural analysis of Wss1 protein from saccharomyces cerevisiae
Cited by: 9
Author(s): Xiaoyun Yang, Yanhua Li, Zengqiang Gao, Zongqiang Li, Jianhua Xu, Wenjia Wang, Yuhui Dong
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.14248

Mutations acquired by hepatocellular carcinoma recurrence give rise to an aggressive phenotype
Cited by: 12
Author(s): Ji-Hye Choi, Min Jae Kim, Yong Keun Park, Jong-Yeop Im, So Mee Kwon, Hyung Chul Kim, Hyun Goo Woo, Hee-Jung Wang
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.15302

Precursor N-cadherin mediates glial cell line-derived neurotrophic factor-promoted human malignant glioma
Cited by: 13
Author(s): Ye Xiong, Liyun Liu, Shuang Zhu, Baole Zhang, Yuxia Qin, Ruiqin Yao, Hao Zhou, Dianshuai Gao
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-08742-z

Identification and Characterization of a Bacterial Homolog of Chloride Intracellular Channel (CLIC) Protein
Cited by: 18
Author(s): Shubha Gururaja Rao, Devasena Ponnalagu, Sowmya Sukur, Harkewal Singh, Shridhar Sanghvi, Yixiao Mei, Ding Jun Jin, Harpreet Singh
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.17207

Eg5 inhibitor YL001 induces mitotic arrest and inhibits tumor proliferation
Cited by: 13
Author(s): Yufei Wang, Xingyu Wu, Mufeng Du, Xi Chen, Xianling Ning, Hong Chen, Siyuan Wang, Jia Liu, Zhenming Liu, Ridong Li, Ge Fu, Chunguang Wang, Michael A. McNutt, Demin Zhou, Yuxin Yin
Software Mentions: 2
Published: over 8 years ago

10.3390/biom10111556

Potential Nutraceutical Properties of Leaves from Several Commonly Cultivated Plants
Cited by: 23
Author(s): Hafsa Amat-ur-Rasool, Fenella Symes, David Tooth, Larissa-Nele Schaffert, Ekramy Elmorsy, Mehboob Ahmed, Shahida Hasnain, Wayne G. Carter
Software Mentions: 2
Published: about 5 years ago

10.3390/molecules24122299

Molecular Informatics Studies of the Iron-Dependent Regulator (ideR) Reveal Potential Novel Anti-Mycobacterium ulcerans Natural Product-Derived Compounds
Cited by: 8
Author(s): Samuel K. Kwofie, Kweku S. Enninful, Jaleel A. Yussif, Lina A. Asante, Mavis Adjei, Kwabena Kan-Dapaah, Elvis K. Tiburu, Wilhelmina A. Mensah, Whelton A. Miller, Lydia Mosi, Michael D. Wilson
Software Mentions: 2
Published: over 6 years ago

10.1016/j.gpb.2017.03.004

Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis
Cited by: 1
Author(s): Zhining Sa, Jingqi Zhou, Yangyun Zou, Zhixi Su, Xun Gu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: over 13 years ago

10.1093/gigascience/gix093

Panax ginseng genome examination for ginsenoside biosynthesis
Cited by: 123
Author(s): Jiang Xu, Yang Chu, Baosheng Liao, Shaobo Xiao, Qinggang Yin, Rui Bai, He Su, Lixin Dong, Xiwen Li, Jun Qian, Jingjing Zhang, Yujun Zhang, Xiaoyan Zhang, Mingli Wu, Jie Zhang, Guozheng Li, Lei Zhang, Zhenzhan Chang, Yuebin Zhang, Zhengwei Jia, Zhixiang Liu, Daniel Ntiamoah Afreh, Ruth Nahurira, Lianjuan Zhang, Ruiyang Cheng, Yingjie Zhu, Guangwei Zhu, Wei Rao, Chao Zhou, Lin Qiao, Zhixing Huang, Yung Chi Cheng, Shilin Chen
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.21652

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab
Cited by: 54
Author(s): Fei Zhang, Xiaoqiang Qi, Xiaoxiao Wang, Diyang Wei, Jiawei Wu, Lingling Feng, Haiyan Cai, Yugang Wang, Naiyan Zeng, Ting Xu, Aiwu Zhou, Ying Zheng
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2021.657970

New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis
Cited by: 26
Author(s): Parviz Heidari, Sahar Faraji, Mostafa Ahmadizadeh, Sunny Ahmar, Freddy Mora‐Poblete
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules23071538

Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile
Cited by: 18
Author(s): Hideaki Niwa, Shin Sato, Tomoko Hashimoto, Kenji Matsuno, Takashi Umehara
Software Mentions: 2
Published: over 7 years ago

10.3390/biom11060798

Mapping the Intramolecular Communications among Different Glutamate Dehydrogenase States Using Molecular Dynamics
Cited by: 4
Author(s): Shaherin Basith, Balachandran Manavalan, Tae Hwan Shin, Gwang Lee
Software Mentions: 2
Published: over 4 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: over 6 years ago

10.1371/journal.pone.0008006

Structure of an Odorant-Binding Protein from the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive “Lid”
Cited by: 103
Author(s): Ney Ribeiro Leite, Renata Krogh, Wei Xü, Yuko Ishida, J. Iulek, Walter S. Leal, Glaucius Oliva
Software Mentions: 2
Published: almost 16 years ago

10.18632/oncotarget.24305

Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells
Cited by: 15
Author(s): Moritz Horn, Virginia Kroef, Kira Allmeroth, Nicole Schuller, Stephan Miethe, Martin Peifer, Josef Penninger, Ulrich Elling, Martin S. Denzel
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-68696-7

Mutational analysis on predicting the impact of high-risk SNPs in human secretary phospholipase A2 receptor (PLA2R1)
Cited by: 6
Author(s): Zoya Khalid, Omar A. Almaghrabi
Software Mentions: 2
Published: over 5 years ago