cran: MM | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.02028

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis
Cited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pgen.1009492

A structural signature motif enlightens the origin and diversification of nuclear receptors
Cited by: 8
Author(s): Brice Beinsteiner, Gabriel V. Markov, Stéphane Erb, Yassmine Chebaro, A.G. McEwen, Sarah Cianférani, Vincent Laudet, Dino Moras, I. M. L. Billas
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2172-9-8

Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research
Cited by: 219
Author(s): Honghuang Lin, Surajit Ray, Songsak Tongchusak, Ellis L. Reinherz, Vladimir Brusic
Software Mentions: 5
Published: almost 17 years ago

10.3390/ijms22179422

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes
Cited by: 28
Author(s): Anna Mazurek, Łukasz Szeleszczuk, Tomasz Gubica
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-54208-9

Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway
Cited by: 5
Author(s): Marina Plotnikova, Sergey A. Klotchenko, Artem Kiselev, А. Н. Горшков, Anna-Polina Shurygina, Kirill Vasilyev, Urszula Uciechowska‐Kaczmarzyk, Sergey A. Samsonov, Alexey L. Kovalenko, А. В. Васин
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5738-6

GScluster: network-weighted gene-set clustering analysis
Cited by: 11
Author(s): Susan A. Yoon, Jinhwan Kim, Seon‐Kyu Kim, Bukyung Baik, Sang-Mun Chi, Seon‐Young Kim, Dougu Nam
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0255803

In silico identification of natural product inhibitors against Octamer-binding transcription factor 4 (Oct4) to impede the mechanism of glioma stem cells
Cited by: 5
Author(s): Chirasmita Nayak, Sanjeev Kumar Singh
Software Mentions: 4
Published: about 3 years ago

10.1038/s41437-021-00412-1

A guide for kernel generalized regression methods for genomic-enabled prediction
Cited by: 12
Author(s): Abelardo Montesinos‐López, Osval A. Montesinos-L֯ópez, J. Cricelio Montesinos-López, Carlos Flores-Cortés, Roberto De Rosa, J. Crossa
Software Mentions: 4
Published: almost 4 years ago

10.3389/fphar.2021.634047

Discovering Potential RNA Dependent RNA Polymerase Inhibitors as Prospective Drugs Against COVID-19: An in silico Approach
Cited by: 16
Author(s): Satabdi Saha, Rajat Nandi, Poonam Vishwakarma, Amresh Prakash, Diwakar Kumar
Software Mentions: 4
Published: almost 4 years ago

10.3390/biom11070929

Discovery of Novel Allosteric Modulators Targeting an Extra-Helical Binding Site of GLP-1R Using Structure- and Ligand-Based Virtual Screening
Cited by: 7
Author(s): Qingtong Zhou, Wei Guo, Antao Dai, Xiaoqing Cai, Márton Vass, Chris de Graaf, Shui Wang, Suwen Zhao, Dehua Yang, Ming Wei Wang
Software Mentions: 3
Published: over 3 years ago

10.1186/s40360-017-0128-7

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
Cited by: 42
Author(s): Matthieu Chartier, Louis–Philippe Morency, María Inés Zylber, Rafaël Najmanovich
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/5314187

To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations
Cited by: 6
Author(s): Holli-Joi Sullivan, Xiaoyan Wang, Shaina Nogle, Susan Liao, Chun Wu
Software Mentions: 3
Published: over 4 years ago

10.1038/srep42765

Duration of SHIV production by infected cells is not exponentially distributed: Implications for estimates of infection parameters and antiviral efficacy
Cited by: 31
Author(s): C. Beauchemin, Tomoyuki Miura, Shingo Iwami
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2019.00009

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data
Cited by: 60
Author(s): Aanchal Mongia, Debarka Sengupta, Angshul Majumdar
Software Mentions: 3
Published: almost 6 years ago

10.3390/pharmaceutics13040554

Artocarpin Targets Focal Adhesion Kinase-Dependent Epithelial to Mesenchymal Transition and Suppresses Migratory-Associated Integrins in Lung Cancer Cells
Cited by: 10
Author(s): Nongyao Nonpanya, Kittipong Sanookpan, Nicharat Sriratanasak, Chanida Vinayanuwattikun, Duangdao Wichadakul, Boonchoo Sritularak, Pithi Chanvorachote
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0169578

Investigation of Inclusion Complex of Patchouli Alcohol with β-Cyclodextrin
Cited by: 6
Author(s): Fangfang Xu, Qiuxia Yang, Li-Lan Wu, Rui Qi, Yunshan Wu, Yucui Li, Lin Tang, De‐An Guo, Bo Liu
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-15-88

Multi-model inference using mixed effects from a linear regression based genetic algorithm
Cited by: 1
Author(s): Koen Van der Borght, Geert Verbeke, Herman van Vlijmen
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0190942

Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants
Cited by: 6
Author(s): Subhash Verma, Sumit Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Abhinav Grover
Software Mentions: 3
Published: almost 7 years ago

10.3389/fchem.2020.597495

Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations
Cited by: 4
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 3
Published: about 4 years ago

10.3390/biomedicines9091197

Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations
Cited by: 9
Author(s): Vikas Kumar, Shraddha Parate, Gunjan Thakur, Gihwan Lee, Hyeon Su Ro, Yong-Seong Kim, Hong Ja Kim, Myeong Ok Kim, Keun Woo Lee
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms21103621

Computational Simulations to Guide Enzyme-Mediated Prodrug Activation
Cited by: 11
Author(s): Milica Marković, Shimon Ben‐Shabat, Arik Dahan
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1006650

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Cited by: 2,164
Author(s): Remco R. Bouckaert, Timothy G. Vaughan, Joëlle Barido‐Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David A. Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Donghua Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0046902

Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study
Cited by: 77
Author(s): Christoph Rademacher, Andrea Spitaleri, Giovanna Musco
Software Mentions: 3
Published: about 12 years ago

10.1186/s13321-017-0254-7

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms
Cited by: 45
Author(s): Ting Feng, Chen Fu, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
Software Mentions: 3
Published: about 7 years ago

10.3389/fmolb.2021.676976

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules
Cited by: 26
Author(s): Marco Giulini, Marta Rigoli, Giovanni Mattiotti, Roberto Menichetti, Thomas Tarenzi, Raffaele Fiorentini, Raffaello Potestio
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules26144323

Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
Cited by: 1
Author(s): Ozren Jović, Tomislav Šmuc
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009384

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2
Cited by: 15
Author(s): Abhisek Dwivedy, Richard Mariadasse, Mohammed Ahmad, Sanjoy Chakraborty, Deepsikha Kar, Satish Tiwari, Sankar Bhattacharyya, Sudipta Sonar, Shailendra Mani, Prafullakumar Tailor, Tanmay Majumdar, Jeyaraman Jeyakanthan, B.K. Biswal
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules25174016

Targeting the Initiator Protease of the Classical Pathway of Complement Using Fragment-Based Drug Discovery
Cited by: 8
Author(s): Blake R. Rushing, Denise L Rohlik, Sourav Roy, D. Andrew Skaff, Brandon L. Garcia
Software Mentions: 3
Published: over 4 years ago

10.3389/fncel.2020.00137

Cellular and Molecular Targets of Waterbuck Repellent Blend Odors in Antennae of Glossina fuscipes fuscipes Newstead, 1910
Cited by: 5
Author(s): Souleymane Diallo, Mohd Shahbaaz, Baldwyn Torto, Alan Christoffels, Daniel Masiga, Merid N. Getahun
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21030965

The Cannabis Proteome Draft Map Project
Cited by: 13
Author(s): Conor Jenkins, Benjamin C. Orsburn
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpsyg.2019.01056

Understanding the Multidimensional Nature of Student Engagement During the First Year of Higher Education
Cited by: 14
Author(s): Vesa Korhonen, Markus Mattsson, Mikko Inkinen, Auli Toom
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2015.00248

Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach
Cited by: 69
Author(s): Chiara Bianca Maria Platania, Luisa Di Paola, Gian Marco Leggio, Giovanni Luca Romano, Filippo Drago, Salvatore Salomone, Claudio Bucolo
Software Mentions: 3
Published: about 9 years ago

10.3390/ijms22137071

Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19
Cited by: 18
Author(s): Satyavani Kaliamurthi, Gurudeeban Selvaraj, Chandrabose Selvaraj, Sanjeev Kumar Singh, Dong Wei, Gilles H. Peslherbe
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0099193

Discovering Functional Modules across Diverse Maize Transcriptomes Using COB, the Co-Expression Browser
Cited by: 26
Author(s): Robert J. Schaefer, Roman Briskine, Nathan M. Springer, Chad L. Myers
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-30420-x

Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer
Cited by: 12
Author(s): Divya Dhasmana, Ashutosh Singh, Rohit Shukla, Timir Tripathi, Neha Garg
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-89627-0

Drug repurposing for ligand-induced rearrangement of Sirt2 active site-based inhibitors via molecular modeling and quantum mechanics calculations
Cited by: 36
Author(s): Shiv Bharadwaj, Amit Dubey, Nitin Kamboj, Amaresh Kumar Sahoo, Sang Gu Kang, Umesh Yadava
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-171

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine
Cited by: 30
Author(s): Christophe Plomion, Émilie Chancerel, Jeffrey B. Endelman, Jean‐Baptiste Lamy, Eric Mandrou, Isabelle Lesur, François Ehrenmann, Fikret Isik, M.C.A.M. Bink, Joost van Heerwaarden, Laurent Bouffier
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-97368-3

Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach
Cited by: 6
Author(s): Sajda Ashraf, Kara E. Ranaghan, Christopher Woods, Adrian J. Mulholland, Zaheer Ul-Haq
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules25153510

In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics
Cited by: 11
Author(s): Rabia Mukhtar Rana, Shailima Rampogu, Noman Bin Abid, Amir Zeb, Shraddha Parate, Gihwan Lee, Sanghwa Yoon, Yumi Kim, Dong Hwan Kim, Keun Woo Lee
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-14916-6

Structural Insight into Inhibition of CsrA-RNA Interaction Revealed by Docking, Molecular Dynamics and Free Energy Calculations
Cited by: 11
Author(s): Xiaodong Ren, Rui Zeng, Micky D. Tortorella, Jinming Wang, Changwei Wang
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-31234-7

Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics
Cited by: 8
Author(s): T Devanand, Prasanna Venkatraman, Satyavani Vemparala
Software Mentions: 2
Published: over 6 years ago

10.3390/s17102433

mlCAF: Multi-Level Cross-Domain Semantic Context Fusioning for Behavior Identification
Cited by: 10
Author(s): Muhammad Asif Razzaq, Claudia Villalonga, Sungyoung Lee, Usman Akhtar, Mohsen Ali, Eun-Soo Kim, Asad Masood Khattak, Hyonwoo Seung, Tae Ho Hur, Jae Hun Bang, Dohyeong Kim, Wajahat Ali Khan
Software Mentions: 2
Published: about 7 years ago

10.1186/s13321-019-0394-z

ACID: a free tool for drug repurposing using consensus inverse docking strategy
Cited by: 47
Author(s): Fan Wang, Feng-Xu Wu, Chengzhang Li, Chen-Yang Jia, Sun-Wen Su, Ge‐Fei Hao, Guang‐Fu Yang
Software Mentions: 2
Published: about 5 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: about 7 years ago

10.1021/acs.jcim.0c00076

Molecular Perception for Visualization and Computation: The Proxima Library
Cited by: 20
Author(s): Federico Lazzari, Andrea Salvadori, Giordano Mancini, Vincenzo Barone
Software Mentions: 2
Published: over 4 years ago

10.3389/fpsyg.2021.662950

Conspicuous Consumption in Emerging Markets: The Case of Starbucks in Colombia as a Global and Sustainable Brand
Cited by: 6
Author(s): Jose Andres Areiza-Padilla, Mario Andres Manzi Puertas
Software Mentions: 2
Published: over 3 years ago

10.3389/fvets.2020.00549

Opinions of Portuguese Veterinarians on Telemedicine—A Policy Delphi Study
Cited by: 4
Author(s): Manuel Magalhães-Sant’Ana, Maria C. Peleteiro, George Stilwell
Software Mentions: 2
Published: over 4 years ago

10.3389/fpsyt.2021.725511

Serum Amyloid Biomarkers, Tau Protein and YKL-40 Utility in Detection, Differential Diagnosing, and Monitoring of Dementia
Cited by: 4
Author(s): Karolina Wilczyńska, Mateusz Maciejczyk, Anna Zalewska, Napoleon Waszkiewicz
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1005441

Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
Cited by: 14
Author(s): Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Li Geng, Qiaojun Fang
Software Mentions: 2
Published: over 7 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: over 11 years ago

10.3389/fphar.2018.01089

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
Cited by: 170
Author(s): Isabella Alvim Guedes, Felipe Siconha S Pereira, Laurent E. Dardenne
Software Mentions: 2
Published: about 6 years ago

10.1038/srep14767

p38 MAPK regulates PKAα and CUB-serine protease in Amphibalanus amphitrite cyprids
Cited by: 5
Author(s): Gen Zhang, Lisheng He, Yue Him Wong, Ying Xü, Yu Zhang, Pei‐Yuan Qian
Software Mentions: 2
Published: about 9 years ago

10.3390/ma6104284

A Hybrid Methacrylate-Sodium Carboxymethylcellulose Interpolyelectrolyte Complex: Rheometry and in Silico Disposition for Controlled Drug Release
Cited by: 22
Author(s): Ndidi C. Ngwuluka, Yahya E. Choonara, Pradeep Kumar, Girish Modi, Lisa C. du Toit, Viness Pillay
Software Mentions: 2
Published: about 11 years ago

10.1186/1472-6807-8-53

Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys
Cited by: 9
Author(s): Dan Bolser, Ioannis Filippis, Henning Stehr, José M. Duarte, Michael Lappé
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12864-018-4461-z

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses
Cited by: 7
Author(s): Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee-Keong Kwoh
Software Mentions: 2
Published: over 6 years ago

10.3390/toxins12120746

Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors
Cited by: 16
Author(s): Fernanda D. Botelho, Marcelo C. dos Santos, Arlan da Silva Gonçalves, Kamil Kuča, Martin Vališ, Steven R. LaPlante, Tanos C. C. França, Joyce S. F. D. de Almeida
Software Mentions: 2
Published: about 4 years ago

10.3389/fphar.2018.00146

QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities
Cited by: 21
Author(s): Marília N. N. Lima, Cleber C. Melo-Filho, Gustavo Capatti Cassiano, Bruno J. Neves, Vinícius M. Alves, Rodolpho C. Braga, Pedro Vitor Lemos Cravo, Eugene Muratov, Juliana Calit, Daniel Youssef Bargieri, Fábio Trindade Maranhão Costa, Carolina Horta Andrade
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-017-16427-w

Allosteric inhibitor remotely modulates the conformation of the orthestric pockets in mutant IDH2/R140Q
Cited by: 18
Author(s): Jiao Chen, Jie Yang, Xianqiang Sun, Zhongming Wang, Xiaolan Cheng, Wei Lü, Xueting Cai, Chunping Hu, Xu Shen, Peng Cao
Software Mentions: 2
Published: about 7 years ago

10.3390/biom9040133

Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in Escherichia coli: Insights from Molecular Dynamics Simulations
Cited by: 12
Author(s): Faiza Gul Durrani, Roquyya Gul, Muhammad Usman Mirza, Naheed Kaderbhai, Matheus Froeyen, M. Saleem
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-48940-5

Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis
Cited by: 15
Author(s): Bharati Pandey, Sonam Grover, Jagdeep Kaur, Abhinav Grover
Software Mentions: 2
Published: over 5 years ago

10.1242/bio.045906

Heterogeneous response of endothelial cells to insulin like growth factor 1 treatment is explained by spatially clustered subpopulations
Cited by: 4
Author(s): Christina Kim, Gregory J. Seedorf, Steven H. Abman, Douglas P. Shepherd
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-77911-4

Cancer associated talin point mutations disorganise cell adhesion and migration
Cited by: 15
Author(s): Latifeh Azizi, Alana R. Cowell, Vasyl V. Mykuliak, Benjamin T. Goult, Paula Turkki, Vesa P. Hytönen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fphar.2018.00864

Discovery and Identification of Pyrazolopyramidine Analogs as Novel Potent Androgen Receptor Antagonists
Cited by: 5
Author(s): Lingyan Wang, Tian-Qing Song, Xin Wang, Jiazhong Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fmolb.2020.576689

Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes
Cited by: 7
Author(s): Jakob Schneider, Rui P. P. L. Ribeiro, Mercedes Alfonso‐Prieto, Paolo Carloni, Alejandro Giorgetti
Software Mentions: 2
Published: over 4 years ago

10.3390/biom9120861

Evaluating Iso-Mukaadial Acetate and Ursolic Acid Acetate as Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase Inhibitors
Cited by: 10
Author(s): Francis Opoku, Penny Poomani Govender, Ofentse Jacob Pooe, Mthokozisi B. C. Simelane
Software Mentions: 2
Published: about 5 years ago

10.3389/fmolb.2019.00147

Glucose-6-Phosphate Upregulates Txnip Expression by Interacting With MondoA
Cited by: 4
Author(s): Xueyun Zhang, Tao Fu, Qian He, Xiang Gao, Yan Luo
Software Mentions: 2
Published: almost 5 years ago

10.3389/fphar.2018.01038

In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato
Cited by: 68
Author(s): Mohd Aamir, Vinay Kumar Singh, Manish Kumar Dubey, Mukesh Meena, Sandeep Kashyap, Sudheer Kumar Katari, Ram Sanmukh Upadhyay, Amineni Umamaheswari, Surendra Singh
Software Mentions: 2
Published: about 6 years ago

10.3390/biom11020160

Computational Insights into the Potential of Withaferin-A, Withanone and Caffeic Acid Phenethyl Ester for Treatment of Aberrant-EGFR Driven Lung Cancers
Cited by: 12
Author(s): Vidhi Malik, Vipul Kumar, Sunil C. Kaul, Renu Wadhwa, Durai Sundar
Software Mentions: 2
Published: almost 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 6 years ago

10.3389/fimmu.2017.00143

Investigating Substitutions in Antibody–Antigen Complexes Using Molecular Dynamics: A Case Study with Broad-spectrum, Influenza A Antibodies
Cited by: 10
Author(s): William D. Lees, Lenka Stejskal, David S. Moss, Adrian J. Shepherd
Software Mentions: 2
Published: almost 8 years ago

10.3389/fchem.2020.628609

In silico Analysis Revealed Potential Anti-SARS-CoV-2 Main Protease Activity by the Zonulin Inhibitor Larazotide Acetate
Cited by: 21
Author(s): Simone Di Micco, Simona Musella, Maria Carmina Scala, Marina Sala, Pietro Campiglia, Giuseppe Bifulco, Alessio Fasano
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12913-020-05111-x

Strengthening prehospital clinical practice guideline implementation in South Africa: a qualitative case study
Cited by: 3
Author(s): Michael McCaul, Taryn Young, Stevan R. Bruijns, Mike Clarke
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules26092430

Coumarin-Chalcone Hybrids as Inhibitors of MAO-B: Biological Activity and In Silico Studies
Cited by: 14
Author(s): Guillermo Moya-Alvarado, Osvaldo Yáñez, Nicole Morales, Angélica González-González, Carlos Areche, Marco T. Núñez, Angélica Fierro, Olimpo García‐Beltrán
Software Mentions: 2
Published: over 3 years ago

10.3389/fchem.2019.00819

Uncovering the Resistance Mechanism of Mycobacterium tuberculosis to Rifampicin Due to RNA Polymerase H451D/Y/R Mutations From Computational Perspective
Cited by: 17
Author(s): Qianqian Zhang, Xiuli An, Hongli Liu, Shuo Wang, Xiao Tong, Huanxiang Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fmed.2021.672629

Phytochemical Moieties From Indian Traditional Medicine for Targeting Dual Hotspots on SARS-CoV-2 Spike Protein: An Integrative in-silico Approach
Cited by: 31
Author(s): V. Umashankar, Sanjay H. Deshpande, Harsha V. Hegde, Ishwar Singh, Debprasad Chattopadhyay
Software Mentions: 2
Published: over 3 years ago

10.1186/s12964-018-0239-9

The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)
Cited by: 23
Author(s): Jiangfeng Du, Yijing Qin, Yahong Wu, Wenshan Zhao, Wenjie Zhai, Yuanming Qi, Chuchu Wang, Jiangfeng Du
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13020356

A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness In Vitro
Cited by: 16
Author(s): Edoardo Luigi Maria Gelardi, Giorgia Colombo, Francesca Picarazzi, Davide M. Ferraris, Andrea Mangione, Giovanni Petrarolo, Eleonora Aronica, Menico Rizzi, Mattia Mori, Concettina La Motta, Silvia Garavaglia
Software Mentions: 2
Published: almost 4 years ago

10.1111/cbdd.12170

Evaluating the Predictivity of Virtual Screening for <scp>A</scp> bl Kinase Inhibitors to Hinder Drug Resistance
Cited by: 7
Author(s): Osman Gani, Dilip Narayanan, Richard A. Engh
Software Mentions: 2
Published: about 11 years ago

10.3390/molecules25225334

Searching Hit Potential Antimicrobials in Natural Compounds Space against Biofilm Formation
Cited by: 5
Author(s): Roberto Pestana-Nobles, Jorge A. Leyva-Rojas, Juvenal Yosa
Software Mentions: 2
Published: about 4 years ago

10.3390/biomedicines8120629

Detailed Characterization of the Cooperative Binding of Piperine with Heat Shock Protein 70 by Molecular Biophysical Approaches
Cited by: 3
Author(s): Gabriel Zazeri, Ana Paula Ribeiro Povinelli, Marcelo de Freitas Lima, Marinônio Lopes Cornélio
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-15-59

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters
Cited by: 102
Author(s): Christopher Funk, William A. Baumgartner, Benjamin J. Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence Hunter, Karin Verspoor
Software Mentions: 2
Published: almost 11 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: over 4 years ago

10.1371/journal.pone.0213217

Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
Cited by: 11
Author(s): José M. Granadino‐Roldán, Antonia S. J. S. Mey, Juan Gonzalez, Stefano Bosisio, Jaime Rubio-Martínez, Julien Michel
Software Mentions: 2
Published: almost 6 years ago

10.3390/molecules26164961

Pharmacophore-Based Virtual Screening, Quantum Mechanics Calculations, and Molecular Dynamics Simulation Approaches Identified Potential Natural Antiviral Drug Candidates against MERS-CoV S1-NTD
Cited by: 32
Author(s): Thamer A. Bouback, Sushil Pokhrel, Abdulaziz Albeshri, Amal Mohammed Aljohani, Abdus Samad, Rahat Alam, Saddam Hossen, Khalid M. AlGhamdi, Enamul Kabir Talukder, Foysal Ahammad, Ishtiaq Qadri, Jesús Simal-Gándara
Software Mentions: 2
Published: over 3 years ago

10.3390/e21070645

Context Based Predictive Information
Cited by: 0
Author(s): Yuval Shalev, Irad Ben‐Gal
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.11552

Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
Cited by: 6
Author(s): Mohini Yadav, Manabu Igarashi, Norifumi Yamamoto
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0238812

One-step automated bioprinting-based method for cumulus-oocyte complex microencapsulation for 3D in vitro maturation
Cited by: 19
Author(s): Antonella Mastrorocco, Ludovica Cacopardo, Nicola Antonio Martino, Diana Fanelli, Francesco Camillo, Elena Ciani, Bernard A. J. Roelen, Arti Ahluwalia, Maria Elena Dell’Aquila
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules25092135

Phenylpyrazalopyrimidines as Tyrosine Kinase Inhibitors: Synthesis, Antiproliferative Activity, and Molecular Simulations
Cited by: 10
Author(s): Bhupender S. Chhikara, Sajda Ashraf, Saghar Mozaffari, Nicole St. Jeans, Dindyal Mandal, Rakesh Tiwari, Zaheer Ul-Haq, Keykavous Parang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0044137

Enhanced Solubilisation of Six PAHs by Three Synthetic Cyclodextrins for Remediation Applications: Molecular Modelling of the Inclusion Complexes
Cited by: 48
Author(s): E. Morillo, M.A. Sánchez-Trujillo, J. R. Moyano, Jaime Villaverde, María Eulalia Gómez-Pantoja, J. I. Pérez-Martínez
Software Mentions: 2
Published: over 12 years ago

10.1155/2020/4932572

Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat’s Claw) against the Main Protease 3CLpro of SARS-CoV-2 by Molecular Modeling
Cited by: 19
Author(s): Andrés F. Yepes-Pérez, Oscar Herrera-Calderon, José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala, Jean‐Didier Maréchal, Wilson Cardona‐G
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0112969

The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
Cited by: 24
Author(s): Seyed Hanif Mahboobi, Alex A. Javanpour, Mohammad R. K. Mofrad
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pcbi.1002011

Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations
Cited by: 70
Author(s): Rilei Yu, David J. Craik, Quentin Kaas
Software Mentions: 2
Published: almost 14 years ago

10.1007/s11682-018-9853-9

Alterations in volumes and MRI features of amygdala in Chinese autistic preschoolers associated with social and behavioral deficits
Cited by: 8
Author(s): Zhiwei Zhu, Xiangming Fang, Hongwei Chen, Xiaogang Zhu, Lili Zhang, Xiaodong Zhai, Zhi-Min Cui, Quansheng Gao
Software Mentions: 2
Published: almost 7 years ago

10.3389/fphar.2018.00395

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities
Cited by: 33
Author(s): Marcelo Depólo Polêto, Victor H. Rusu, Bruno Iochins Grisci, Márcio Dorn, Roberto D. Lins, Hugo Verli
Software Mentions: 2
Published: over 6 years ago

10.3390/molecules24173125

Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling
Cited by: 4
Author(s): Imane Bjij, Pritika Ramharack, Shama Khan, Driss Cherqaoui, Mahmoud E. S. Soliman
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-4930-4

A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)
Cited by: 34
Author(s): Maryam Rahmati Ishka, Elizabeth Brown, Chrystle Weigand, Richard L. Tillett, Karen Schlauch, Gad Miller, Jeffrey F. Harper
Software Mentions: 2
Published: over 6 years ago

10.1002/mrm.26778

Simultaneous mapping of metabolites and individual macromolecular components via ultra-short acquisition delay<sup>1</sup>H MRSI in the brain at 7T
Cited by: 43
Author(s): Michal Považan, Bernhard Strasser, Gilbert Hangel, Eva Hečková, Stephan Gruber, Siegfried Trattnig, Wolfgang Bogner
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0219926

Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects
Cited by: 14
Author(s): Anshuman Sewda, A. J. Agopian, Elizabeth Goldmuntz, Hákon Hákonarson, Bernice E. Morrow, Deanne Taylor, Laura E. Mitchell
Software Mentions: 2
Published: over 5 years ago

10.1002/mrm.28196

Diffusion model comparison identifies distinct tumor sub‐regions and tracks treatment response
Cited by: 5
Author(s): Damien J. McHugh, Grazyna Lipowska‐Bhalla, Muhammad Babur, Yvonne Watson, Isabel Peset, Hitesh Mistry, Penny L. Hubbard Cristinacce, Josephine H. Naish, Jamie Honeychurch, Kaye J. Williams, James P.B. O’Connor, Geoffrey Parker
Software Mentions: 2
Published: almost 5 years ago

10.1107/S205979831900175X

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data
Cited by: 13
Author(s): Octav Caldararu, Francesco Manzoni, Esko Oksanen, D.T. Logan, Ulf Ryde
Software Mentions: 2
Published: over 5 years ago

Projects: cran: MM

Papers Mentioning MM 314