Ecosyste.ms: Papers

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

10.1186/2046-1682-6-10

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

10.1038/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/s41598-017-16427-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: almost 7 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

10.1038/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: about 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: about 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

10.3390/e21060551

MEMe: An Accurate Maximum Entropy Method for Efficient Approximations in Large-Scale Machine Learning
Cited by: 15
Author(s): Diego Granziol, Binxin Ru, Stefan Zohren, Xiaowen Doing, Michael A. Osborne, Stephen Roberts
Software Mentions: 1
Published: over 5 years ago

10.1007/s00259-018-4140-y

Improved beta-amyloid PET reproducibility using two-phase acquisition and grey matter delineation
Cited by: 4
Author(s): Otakar Bělohlávek, Monika Jaruskova, Magdaléna Skopalová, Gabriela Szarazova, Kateřina Šimonová
Software Mentions: 1
Published: about 6 years ago

10.3389/fchem.2019.00602

Structural, Thermodynamic, and Kinetic Traits of Antiestrogen-Compounds Selectively Targeting the Y537S Mutant Estrogen Receptor α Transcriptional Activity in Breast Cancer Cell Lines
Cited by: 6
Author(s): Matic Pavlin, Luca Gelsomino, Ines Barone, Angelo Spinello, Stefania Catalano, Sebastiano Andò, Alessandra Magistrato
Software Mentions: 1
Published: about 5 years ago

10.3389/fchem.2018.00070

Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code
Cited by: 25
Author(s): Juan P. Marcolongo, Ari Zeida, Jonathan A. Semelak, Nicolás O. Foglia, Uriel N. Morzan, Darı́o A. Estrin, Mariano C. González Lebrero, Damián A. Scherlis
Software Mentions: 1
Published: over 6 years ago

10.3389/fchem.2018.00089

On the Difference Between Additive and Subtractive QM/MM Calculations
Cited by: 68
Author(s): Lili Cao, Ulf Ryde
Software Mentions: 1
Published: over 6 years ago

10.3389/fchem.2018.00062

Chloride Ion Transport by the E. coli CLC Cl−/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study
Cited by: 9
Author(s): Chun‐Hung Wang, Adam W. Duster, Baris O. Aydintug, MacKenzie G. Zarecki, Hai Lin
Software Mentions: 1
Published: over 6 years ago

10.3389/fchem.2020.00246

High-Throughput Docking Using Quantum Mechanical Scoring
Cited by: 33
Author(s): Claudio N. Cavasotto, María Gabriela Aucar
Software Mentions: 1
Published: over 4 years ago

10.3389/fchem.2020.589769

Screening of Natural Products Targeting SARS-CoV-2–ACE2 Receptor Interface – A MixMD Based HTVS Pipeline
Cited by: 14
Author(s): Krishnasamy Gopinath, Elmeri M. Jokinen, Sami T. Kurkinen, Olli T. Pentikäinen
Software Mentions: 1
Published: about 4 years ago

10.3389/fchem.2019.00536

The Role of Proton Transfer on Mutations
Cited by: 38
Author(s): Ruby Srivastava
Software Mentions: 1
Published: over 5 years ago

10.3389/fchem.2018.00043

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings
Cited by: 47
Author(s): Irene Maffucci, Xiao Hu, Valentina Fumagalli, Alessandro Contini
Software Mentions: 1
Published: over 6 years ago

10.3389/fchem.2020.00425

Molecular Determinants Elucidate the Selectivity in Abscisic Acid Receptor and HAB1 Protein Interactions
Cited by: 10
Author(s): Jing‐Fang Yang, Chunyan Yin, Di Wang, Chen-Yang Jia, Ge‐Fei Hao, Guang‐Fu Yang
Software Mentions: 1
Published: over 4 years ago

10.3389/fchem.2019.00764

Computational Insight Into the Small Molecule Intervening PD-L1 Dimerization and the Potential Structure-Activity Relationship
Cited by: 29
Author(s): Danfeng Shi, Xiuli An, Qifeng Bai, Zhitong Bing, Shuangyan Zhou, Huanxiang Liu, Xiaojun Yao
Software Mentions: 1
Published: about 5 years ago

10.3389/fchem.2018.00105

Peptide Modified ZnO Nanoparticles as Gas Sensors Array for Volatile Organic Compounds (VOCs)
Cited by: 38
Author(s): Marcello Mascini, Sara Gaggiotti, Flavio Della Pelle, Corrado Di Natale, Sinazo Qakala, Emmanuel I. Iwuoha, Paola Pittia, Darío Compagnone
Software Mentions: 1
Published: over 6 years ago

10.3389/fmed.2020.547186

Genetic Susceptibility to Antisynthetase Syndrome Associated With Single-Nucleotide Variants in the IL1B Gene That Lead Variation in IL-1β Serum Levels
Cited by: 8
Author(s): Marco Antonio Ponce-Gallegos, Espiridión Ramos-Martı́nez, Adriana García-Carmona, Mayra Mejía, Karol J. Nava-Quiroz, Gloría Pérez-Rubio, Enrique Ambrocio-Ortiz, Montserrat I. González-Pérez, Ivette Buendía-Roldán, Jorge Rojas-Serrano, Ramcés Falfán-Valencia
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.592908

Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2
Cited by: 57
Author(s): Ahmad F. Eweas, Amr Alhossary, Ahmed S. Abdel‐Moneim
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2021.703145

Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System
Cited by: 18
Author(s): Farooq Rashid, Muhammad Suleman, Abdullah Shah, Emmanuel Enoch Dzakah, Haiying Wang, Shuyi Chen, Shixing Tang
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2020.626363

Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences
Cited by: 50
Author(s): Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmolb.2016.00046

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking
Cited by: 58
Author(s): Christoph Rademacher, Panagiotis L. Kastritis, Adrien Melquiond, Alexandre Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Software Mentions: 1
Published: about 8 years ago

10.3389/fmolb.2017.00101

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field
Cited by: 3
Author(s): Jian Chen, Lili Duan, Changge Ji, John Z. H. Zhang
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmolb.2021.655035

Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation
Cited by: 8
Author(s): Shraddha Parate, Shailima Rampogu, Gihwan Lee, Jong Chan Hong, Keun Woo Lee
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2019.00029

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations
Cited by: 27
Author(s): Mercedes Alfonso‐Prieto, Luciano Navarini, Paolo Carloni
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2018.00064

The Impairment of TorsinA's Binding to and Interactions With Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia
Cited by: 16
Author(s): Emmanuel Oluwatobi Salawu
Software Mentions: 1
Published: over 6 years ago

10.3389/fnmol.2018.00347

Modification of a Putative Third Sodium Site in the Glycine Transporter GlyT2 Influences the Chloride Dependence of Substrate Transport
Cited by: 14
Author(s): Cristina Benito-Muñoz, Almudena Perona, David Abia, Helena Santos, Enrique Núñez, Carmen Aragón, Beatriz Lopez‐Corcuera
Software Mentions: 1
Published: about 6 years ago

10.3389/fneur.2021.696276

Motor Imagery: A Resource in the Fatigue Rehabilitation for Return-to-Work in Multiple Sclerosis Patients—A Mini Systematic Review
Cited by: 10
Author(s): Francesco Agostini, Letizia Pezzi, Marco Paoloni, Roberta Insabella, Carmine Attanasi, Andrea Bernetti, Raoul Saggini, Massimiliano Mangone, Teresa Paolucci
Software Mentions: 1
Published: over 3 years ago

10.3389/fnins.2019.00008

In Praise of Artifice Reloaded: Caution With Natural Image Databases in Modeling Vision
Cited by: 11
Author(s): Marina Martínez-Garcia, Marcelo Bertalmío, Jesús Malo
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2020.00971

ULBP1 Is Elevated in Human Hepatocellular Carcinoma and Predicts Outcome
Cited by: 10
Author(s): Nicholas Easom, Michael Marks, Dawda Jobe, Roopinder Gillmore, Tim Meyer, Mala K. Maini, Ramou Njie
Software Mentions: 1
Published: over 4 years ago

10.3389/fphar.2019.01582

Identification of a Selective PDE4B Inhibitor From Bryophyllum pinnatum by Target Fishing Study and In Vitro Evaluation of Quercetin 3-O-α-L-Arabinopyranosyl-(1→2)-O-α-L-Rhamnopyranoside
Cited by: 9
Author(s): Estela Mariana Guimarães Lourenço, Júlia Morais Fernandes, Vinícius F. Carvalho, Raphaë͏l Grougnet, Marco A. Martins, Alessandro K. Jordão, Silvana Maria Zucolotto, Euzébio Guimarães Barbosa
Software Mentions: 1
Published: almost 5 years ago

10.3389/fphar.2019.01050

Insights Into the Resistance Mechanisms of Inhibitors to FLT3 F691L Mutation via an Integrated Computational Approach
Cited by: 1
Author(s): Yihong Sun, Zhongni Xia, Qinqin Zhao, Bei Zheng, Meiling Zhang, Ying Yin
Software Mentions: 1
Published: about 5 years ago

10.3389/fphar.2021.701568

Evaluation of the IKKβ Binding of Indicaxanthin by Induced-Fit Docking, Binding Pose Metadynamics, and Molecular Dynamics
Cited by: 20
Author(s): Mario Allegra, Marco Tutone, Luisa Tesoriere, Alessandro Attanzio, Giulia Culletta, Anna Maria Almerico
Software Mentions: 1
Published: about 3 years ago

10.3389/fphar.2019.00345

Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I1/2 NIK Inhibitors
Cited by: 11
Author(s): Chao Shen, Hui Liu, Xuwen Wang, Tailong Lei, Ercheng Wang, Lei Xu, Huidong Yu, Dan Li, Xiaojun Yao
Software Mentions: 1
Published: over 5 years ago

10.3389/fpsyt.2013.00071

Meditative Movement for Depression and Anxiety
Cited by: 80
Author(s): Peter Payne, Mardi A. Crane-Godreau
Software Mentions: 1
Published: almost 12 years ago

10.3389/fpsyg.2020.584320

SARS-CoV-2 and Asbestos Exposure: Can Our Experience With Mesothelioma Patients Help Us Understand the Psychological Consequences of COVID-19 and Develop Interventions?
Cited by: 10
Author(s): Antonella Granieri, Michela Bonafede, Alessandro Marinaccio, Ivano Iavarone, Daniela Marsili, Isabella Giulia Franzoi
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.heliyon.2018.e01021

Drug discovery of anticancer drugs targeting methylenetetrahydrofolate dehydrogenase 2
Cited by: 22
Author(s): Ayumu Asai, Junichi Koseki, Masamitsu Konno, Tatsunori Nishimura, Noriko Gotoh, Taroh Satoh, Yuichiro Doki, Masaki Mori, Hideshi Ishii
Software Mentions: 1
Published: almost 6 years ago

10.14440/jbm.2016.138

CRISPR Explorer: A fast and intuitive tool for designing guide RNA for genome editing
Cited by: 4
Author(s): Kenian Chen, Yi Jin, Yin Lin
Software Mentions: 1
Published: about 8 years ago

10.1021/acs.jcim.1c00414

All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric Peptide
Cited by: 3
Author(s): Eva Prašnikar, Andrej Perdih, Jure Borišek
Software Mentions: 1
Published: over 3 years ago

10.1002/jcc.23839

The adaptive buffered force <scp>QM/MM</scp> method in the <scp>CP2K</scp> and <scp>AMBER</scp> software packages
Cited by: 38
Author(s): Letif Mones, Andrew Jones, Andreas W. Götz, Teodoro Laino, Ross C. Walker, Benedict Leimkuhler, Gábor Csänyi, Noam Bernstein
Software Mentions: 1
Published: almost 10 years ago

10.1155/2012/579629

Composite Polylactic-Methacrylic Acid Copolymer Nanoparticles for the Delivery of Methotrexate
Cited by: 21
Author(s): Bongani Sibeko, Yahya E. Choonara, Lisa C. du Toit, Girish Modi, Dinesh Naidoo, Riaz Khan, Pradeep Kumar, Valence M. K. Ndesendo, Sunny E. Iyuke, Viness Pillay
Software Mentions: 1
Published: over 12 years ago

10.1080/14756366.2019.1571271

Computationally driven discovery of phenyl(piperazin-1-yl)methanone derivatives as reversible monoacylglycerol lipase (MAGL) inhibitors
Cited by: 27
Author(s): Giulio Poli, Margherita Lapillo, Vibhu Jha, Nayla Mouawad, Isabella Caligiuri, Marco Macchia, Filippo Minutolo, Flavio Rizzolio, Tiziano Tuccinardi, Tiziano Tuccinardi
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.ppat.1003038

HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome
Cited by: 24
Author(s): John M. O’Dowd, Anamaria G. Zavala, Celeste J. Brown, Toshio Mori, Elizabeth A. Fortunato
Software Mentions: 1
Published: almost 12 years ago

10.3390/polym12040881

Hydrogen Bonding in a l-Glutamine-Based Polyamidoamino Acid and its pH-Dependent Self-Ordered Coil Conformation
Cited by: 4
Author(s): F. Lazzari, Amedea Manfredi, Jenny Alongi, Fabio Ganazzoli, Francesca Vasile, Giuseppina Raffaini, Paolo Ferruti, Elisabetta Ranucci
Software Mentions: 1
Published: over 4 years ago

10.1002/prot.24230

<i>p</i>H‐selective mutagenesis of protein–protein interfaces:<i>In silico</i>design of therapeutic antibodies with prolonged half‐life
Cited by: 56
Author(s): Velin Z. Spassov, Lisa Yan
Software Mentions: 1
Published: almost 12 years ago

10.21203/rs.3.rs-871118/v1

The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2
Cited by: 3
Author(s): Yixin Xie, Wenhan Guo, Alan Lopez-Hernadez, Shaolei Teng, Lin Li
Software Mentions: 1
Published: about 3 years ago

10.1126/sciadv.abb8097

Structure-based drug designing and immunoinformatics approach for SARS-CoV-2
Cited by: 129
Author(s): Pritam Kumar Panda, Natarajan Arul Murugan, Paritosh Patel, Suresh K. Verma, Wei Luo, Horst Gönter Rubahn, Yogendra Kumar Mishra, Mrutyunjay Suar, Rajeev Ahuja
Software Mentions: 1
Published: over 4 years ago

10.1007/s11948-017-9877-3

Organizing a Collaborative Development of Technological Design Requirements Using a Constructive Dialogue on Value Profiles: A Case in Automated Vehicle Development
Cited by: 8
Author(s): Steven M. Flipse, Steven Puylaert
Software Mentions: 1
Published: over 7 years ago

10.1007/s11948-020-00251-z

Integrating Value Considerations in the Decision Making for the Design of Biorefineries
Cited by: 8
Author(s): Mar Palmeros Parada, Lotte Asveld, Patrícia Osseweijer, John A. Posada
Software Mentions: 1
Published: over 4 years ago

10.1038/srep08457

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
Cited by: 71
Author(s): Huiyong Sun, Sheng Tian, Shunye Zhou, Youyong Li, Dan Li, Lei Xu, Meifen Shen, Peichen Pan, Tingjun Hou
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep12359

Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays
Cited by: 27
Author(s): Jiyuan Liu, Xien Chen, Yalin Zhang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12632

Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases
Cited by: 15
Author(s): Wei Ren, Tan Minh Truong, Hui‐wang Ai
Software Mentions: 1
Published: over 9 years ago

10.1038/srep18987

Discovering new mTOR inhibitors for cancer treatment through virtual screening methods and in vitro assays
Cited by: 37
Author(s): Ling Wang, Lei Chen, Miao Yu, Lihui Xu, Bao Cheng, Yongsheng Lin, Qiong Gu, Xian-Hui He, Jing Xu
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep19841

Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin
Cited by: 23
Author(s): Xiaofen Liu, Pei-Jin Pai, Weipeng Zhang, Yingwei Hu, Xiaojing Dong, Pei‐Yuan Qian, Daijie Chen, Henry H N Lam
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep29931

Lupin Peptides Modulate the Protein-Protein Interaction of PCSK9 with the Low Density Lipoprotein Receptor in HepG2 Cells
Cited by: 66
Author(s): Carmen Lammi, Chiara Zanoni, Gilda Aiello, Anna Arnoldi, Giovanni Grazioso
Software Mentions: 1
Published: over 8 years ago

10.1038/srep31418

Understanding the molecular basis of substrate binding specificity of PTB domains
Cited by: 7
Author(s): Neetu Sain, Garima Tiwari, Debasisa Mohanty
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34516

Computational prediction shines light on type III secretion origins
Cited by: 34
Author(s): Tatyana Goldberg, Burkhard Rost, Yana Bromberg
Software Mentions: 1
Published: about 8 years ago

10.1038/srep37584

Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations
Cited by: 96
Author(s): Zhicheng Zuo, Jin Liu
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep41675

Magnetocaloric effect and negative thermal expansion in hexagonal Fe doped MnNiGe compounds with a magnetoelastic AFM-FM-like transition
Cited by: 36
Author(s): Xu Kuangdi, Zhe Li, Enke Liu, Haichun Zhou, Yuanlei Zhang, Chao Jing
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep42223

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations
Cited by: 17
Author(s): Li L. Duan, Tong Zhu, Yu C. Li, Qing G. Zhang, John Z. H. Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep42057

Lumican Peptides: Rational Design Targeting ALK5/TGFBRI
Cited by: 27
Author(s): Tarsis F. Gesteira, Vivien Jane Coulson‐Thomas, Yong Yuan, Jianhua Zhang, Helena B. Nader, Winston W.‐Y. Kao
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep46547

Revealing inhibition difference between PFI-2 enantiomers against SETD7 by molecular dynamics simulations, binding free energy calculations and unbinding pathway analysis
Cited by: 22
Author(s): Yuzhen Niu, Danfeng Shi, Lanlan Li, Jingyun Guo, Huanxiang Liu, Xiaojun Yao
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-09586-3

How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study
Cited by: 15
Author(s): Xiaotian Kong, Huiyong Sun, Peichen Pan, Dan Li, Feng Zhu, Shan Chang, Lei Xu, Youyong Li, Tingjun Hou
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-26105-0

Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor
Cited by: 8
Author(s): Liyun Zhang, Yuan Yuan, Tian Heng Ren, Yanzhi Guo, Chuan Li, Xuemei Pu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-26812-8

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Cited by: 18
Author(s): Chen Keasar, McGuffin Lj, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Linda Blake, Bortot Lo, Ruibing Cao, Dhanasekaran Bk, Isabel Dórdio Dimas, Faccioli Ra, Eshel Faraggi, Robert Ganzynkowicz, Soma Ghosh, Artur Giełdoń, Łukasz Golon, Yiliang He, Lim Heo, Jing Hou, Muhammad Usman Ghani Khan, Firas Khatib, Khoury Ga, Chris A. Kieslich, Kim De, Paweł Krupa, Lee Gr, Li H, Jian Li, Agnieszka G. Lipska, Adam Liwo, Maghrabi Aha, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, С. Г. Овчинников, Akash Shah, Urvi Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena J. Ślusarz, Rafał Ślusarz, James B. Smadbeck, Phanourios Tamamis, N Trieber, Tomasz Wirecki, Yuan‐Qi Yin, Y Zhang, Jaume Bacardit, Maciej Baranowski, Nicola H. Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartłomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Acb Delbem, Christodoulos A. Floudas, A. Kloczkowski, Stanisław Ołdziej, Michael Levitt, Harold A. Scheraga, Chaok Seok, Johannes Söding, S. Vishveshwara, Xu D, Crivelli Sn
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-33963-1

Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC
Cited by: 4
Author(s): Eva‐Maria Krammer, Andrew Gibbons, Goedele Roos, Martine Prévost
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-35819-0

Biological Characterization of Computationally Designed Analogs of peptide TVFTSWEEYLDWV (Pep2-8) with Increased PCSK9 Antagonistic Activity
Cited by: 15
Author(s): Carmen Lammi, Jacopo Sgrignani, Anna Arnoldi, Giovanni Grazioso
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-46496-y

Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts
Cited by: 9
Author(s): Angela Koch, Michele Bonus, Holger Gohlke, Nikolaj Klöcker
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-47381-4

Computational Models Accurately Predict Multi-Cell Biomarker Profiles in Inflammation and Cancer
Cited by: 6
Author(s): Carol L. Fischer, Amber M. Bates, Emily A. Lanzel, Janet M. Guthmiller, Georgia K. Johnson, Neeraj Singh, Ansu Kumar, Robinson Vidva, Taher Abbasi, Shireen Vali, Xian Jin Xie, Erliang Zeng, Kim A. Brogden
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-51676-x

The “MYOCYTER” – Convert cellular and cardiac contractions into numbers with ImageJ
Cited by: 21
Author(s): Tilman Grune, Christiane Ott, Steffen Häseli, Annika Höhn, Tobias Jung
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-61494-1

Accelerated identification of serine racemase inhibitor from Centella asiatica
Cited by: 8
Author(s): Komal Rani, Mitali Tyagi, Mohit Mazumder, Akanksha Singh, Annaian Shanmugam, Krishna Dalal, M. Armugam Pillai, S. Gourinath, Saroj Kumar, Alagiri Srinivasan
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-67283-0

DREAM-in-CDM Approach and Identification of a New Generation of Anti-inflammatory Drugs Targeting mPGES-1
Cited by: 11
Author(s): Shuo Zhou, Ziyuan Zhou, Kai Ding, Yaxia Yuan, Charles D. Loftin, Fang Zheng, Chengjun Zhan
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-69515-9

Peptides targeting dengue viral nonstructural protein 1 inhibit dengue virus production
Cited by: 16
Author(s): Pucharee Songprakhon, Thanawat Thaingtamtanha, Thawornchai Limjindaporn, Chunya Puttikhunt, Chatchawan Srisawat, Prasit Luangaram, Thanyaporn Dechtawewat, Chairat Uthaipibull, Sissades Thongsima, Pa‐thai Yenchitsomanus, Prida Malasit, Sansanee Noisakran
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-82889-8

Overcoming Pavlovian bias in semantic space
Cited by: 4
Author(s): Sam Ereira, Marine Pujol, Marc Guitart-Masip, Raymond J. Dolan, Zeb Kurth‐Nelson
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-86712-2

Computational drug repurposing study elucidating simultaneous inhibition of entry and replication of novel corona virus by Grazoprevir
Cited by: 22
Author(s): Santosh Kumar Behera, Nazmina Vhora, Darshan Contractor, Amit Shard, Dinesh Kumar, Kiran Kalia, Alok Jain
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-90167-w

Assessment of select synthetic cannabinoid receptor agonist bias and selectivity between the type 1 and type 2 cannabinoid receptor
Cited by: 17
Author(s): Ayat Zagzoog, Asher L. Brandt, Tallan Black, Eunhyun D. Kim, Riley Burkart, Mikin Patel, Zhiyun Jin, Maria Nikolaeva, Robert B. Laprairie
Software Mentions: 1
Published: over 3 years ago

10.3390/s21051724

Two-Phase Robust Target Localization in Ocean Sensor Networks Using Received Signal Strength Measurements
Cited by: 4
Author(s): Yuanyuan Zhang, Huafeng Wu, Xiaojun Mei, Jiangfeng Xian, Weijun Wang, Qiannan Zhang, Linian Liang
Software Mentions: 1
Published: over 3 years ago

10.1002/sim.8778

The implications of <scp>noncompliance</scp> for randomized trials with partial nesting due to group treatment
Cited by: 3
Author(s): Chris Roberts
Software Mentions: 1
Published: about 4 years ago

10.1063/1.5068756

Intermittent plasticity in individual grains: A study using high energy x-ray diffraction
Cited by: 19
Author(s): Kamalika Chatterjee, Armand Joseph Beaudoin, Darren C. Pagan, Paul A. Shade, Hugh T. Philipp, Mark W. Täte, Sol M. Grüner, Péter Kenesei, Jun-Sang Park
Software Mentions: 1
Published: almost 6 years ago

10.1111/tops.12506

How Intractability Spans the Cognitive and Evolutionary Levels of Explanation
Cited by: 8
Author(s): Patricia Rich, Mark Blokpoel, Ronald de Haan, Iris van Rooij
Software Mentions: 1
Published: over 4 years ago

10.3390/toxins13030193

Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations
Cited by: 8
Author(s): Dana Katz, Daniel J. Sindhikara, Michael A. DiMattia, Abba E. Leffler
Software Mentions: 1
Published: over 3 years ago

10.3906/kim-1911-57

Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors
Cited by: 2
Author(s): Kader Şahin, Serdar Durdağı
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00288-20

T3SEpp: an Integrated Prediction Pipeline for Bacterial Type III Secreted Effectors
Cited by: 21
Author(s): Xinjie Hui, Zewei Chen, Mingxiong Lin, Junya Zhang, Yueming Hu, Yingying Zeng, Xi Cheng, Le Ou-Yang, Ming-an Sun, Aaron P. White, Wang Yejun
Software Mentions: 1
Published: about 4 years ago

10.1107/S2052252517015548

Probing the accuracy and precision of Hirshfeld atom refinement with <i>HARt</i> interfaced with <i>Olex2</i>
Cited by: 68
Author(s): Malte Fugel, Dylan Jayatilaka, Emanuel Hupf, Jacob Overgaard, Venkatesha R. Hathwar, Piero Macchi, Michael J. Turner, Judith A. K. Howard, Oleg V. Dolomanov, Horst Puschmann, Bo B. Iversen, Hans Beat Bürgi, Simon Grabowsky
Software Mentions: 1
Published: almost 7 years ago

10.1107/S2052252519007358

Energetics of interactions in the solid state of 2-hydroxy-8-<i>X</i>-quinoline derivatives (<i>X</i> = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements
Cited by: 9
Author(s): Magdalena Woińska, Monika Wanat, Przemysław Taciak, Tomasz Pawiński, Władek Minor, Krzysztof Woźniak
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.37610

The adhesion function of the sodium channel beta subunit (β1) contributes to cardiac action potential propagation
Cited by: 83
Author(s): Rengasayee Veeraraghavan, Gregory S. Hoeker, Anita Alvarez-Laviada, Daniel Hoagland, Xiaoping Wan, Dennis King, Jose L. Sanchez-Alonso, Chunling Chen, Jane Jourdan, Lori L. Isom, Isabelle Deschênes, J. D. Smyth, Julia Gorelik, Steven Poelzing, Robert G. Gourdie
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.31481

The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome
Cited by: 93
Author(s): Emma A. Morrison, Samuel Bowerman, Kelli L Sylvers, Jeff Wereszczynski, Catherine A. Musselman
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.39476

The molecular basis for an allosteric inhibition of K+-flux gating in K2P channels
Cited by: 20
Author(s): Susanne Rinné, Aytuğ K. Kiper, Kirsty S Vowinkel, David Ramírez, Marcus Schewe, Mauricio Bedoya, Diana Aser, Isabella Gensler, Michael F. Netter, Phillip J. Stansfeld, Thomas Baukrowitz, Wendy González, Niels Decher
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms13022176

Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations
Cited by: 22
Author(s): Jianzhong Chen, Dinglin Zhang, Yuxin Zhang, Guohui Li
Software Mentions: 1
Published: almost 13 years ago

10.3390/ijms17071131

Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study
Cited by: 5
Author(s): Jesús Vicente de Julián-Ortiz, Begoña Verdejo, Víctor Polo, Emili Besalú, Enrique Garcı́a-España
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms20102489

Virtual Screening Guided Design, Synthesis and Bioactivity Study of Benzisoselenazolones (BISAs) on Inhibition of c-Met and Its Downstream Signalling Pathways
Cited by: 6
Author(s): Si-Qi Zhang, Qiaoling Song, Xueting Wang, Zhiqiang Wei, Rilei Yu, Xin Wang, Tao Jiang
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20153840

The Development of Tetrazole Derivatives as Protein Arginine Methyltransferase I (PRMT I) Inhibitors
Cited by: 7
Author(s): Yutong Sun, Zhe Wang, Hao Yang, Xuanli Zhu, Hanjiang Wu, Lu Ma, Fang Xu, Wei Hong, Hao Wang
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20205021

Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction
Cited by: 11
Author(s): Jan Potthoff, Krzysztof K. Bojarski, Gergely Kohut, Agnieszka G. Lipska, Adam Liwo, Efrat Kessler, Sylvie Ricard‐Blum, Sergey A. Samsonov
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20215410

Insights into the Interaction Mechanisms of the Proviral Integration Site of Moloney Murine Leukemia Virus (Pim) Kinases with Pan-Pim Inhibitors PIM447 and AZD1208: A Molecular Dynamics Simulation and MM/GBSA Calculation Study
Cited by: 16
Author(s): Qingqing Chen, Yan Wang, Shanshan Shi, Kaihang Li, Ling Zhang, Jian Gao
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21010005

Tetrahydroquinoline-Isoxazole/Isoxazoline Hybrid Compounds as Potential Cholinesterases Inhibitors: Synthesis, Enzyme Inhibition Assays, and Molecular Modeling Studies
Cited by: 5
Author(s): Yeray A. Rodríguez‐Núñez, Margarita Gutiérrez, Jans Alzate‐Morales, Francisco Adasme‐Carreño, Fausto M. Güiza, Cristian C. Bernal, Arnold R. Romero Bohórquez
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms21155546

Based on the Virtual Screening of Multiple Pharmacophores, Docking and Molecular Dynamics Simulation Approaches toward the Discovery of Novel HPPD Inhibitors
Cited by: 18
Author(s): Ying Fu, Tong Ye, Yongxuan Liu, Jian Wang, Fei Ye
Software Mentions: 1
Published: over 4 years ago