10.1074/jbc.M113.543546

Evidence for Steric Regulation of Fibrinogen Binding to Staphylococcus aureus Fibronectin-binding Protein A (FnBPA)
Cited by: 29
Author(s): Vaclav Stemberk, Richard Jones, Olga V. Moroz, Kate E. Atkin, Andrew M. Edwards, J.P. Turkenburg, Andrew Leech, Ruth C. Massey, Jennifer R. Potts
Software Mentions: 2
Published: over 11 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

10.3389/fphar.2021.697704

Exploring the Potential Molecular Mechanism of Scutellaria baicalensis Georgi in the Treatment of Gastric Cancer Based on Network Pharmacological Analysis and Molecular Docking Technology
Cited by: 12
Author(s): Yi Tu, Qiong Wu, Jiarui He, Jiasheng Xu, Shasha Yu, Qingfei Wang, Yunqi Cheng, Qijun Yang, Shan Xu, Yi Cao
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules25102404

Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli
Cited by: 2
Author(s): Giang T. Nguyen, Yeon-Gil Kim, Joo‐Myung Ahn, Jeong Ho Chang
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2020.561834

Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAA Receptor by Molecular Modeling
Cited by: 3
Author(s): Natesh Singh, Bruno O. Villoutreix
Software Mentions: 2
Published: about 5 years ago

10.3389/fphar.2018.00834

QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop
Cited by: 9
Author(s): Alexander Zlobin, Yuliana A. Mokrushina, Stanislav S. Terekhov, Arthur O. Zalevsky, Т. В. Бобик, A. V. Stepanova, Maria Aliseychik, Olga V. Kartseva, С. В. Пантелеев, Andrey V. Golovin, Alexey A. Belogurov, Alexander G. Gabibov, Иван Смирнов
Software Mentions: 2
Published: over 7 years ago

10.1074/jbc.M114.611780

Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites
Cited by: 53
Author(s): Kye‐Won Kim, Clyde A. Smith, Michael D. Daily, John Cort, Laurence B. Davin, Norman G. Lewis
Software Mentions: 2
Published: almost 11 years ago

10.3389/fphar.2020.00246

Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound
Cited by: 5
Author(s): Emilee E. Colón-Lorenzo, Daisy D. Colón-López, Joel Vega-Rodríguez, Alice Dupin, David A. Fidock, Abel Baerga‐Ortiz, José G. Ortíz, Jürgen Bosch, Adelfa E. Serrano
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2020.00526

Kaempferol, a Major Flavonoid in Ginkgo Folium, Potentiates Angiogenic Functions in Cultured Endothelial Cells by Binding to Vascular Endothelial Growth Factor
Cited by: 26
Author(s): Weihui Hu, Huaiyou Wang, Yiteng Xia, Diana Dai, Qingping Xiong, Tina Tingxia Dong, Ran Duan, Gallant Kar-Lun Chan, Qi Qin, Karl Wah-Keung Tsim
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2018.00008

Suppressive Effects of Clerodendrum volubile P Beauv. [Labiatae] Methanolic Extract and Its Fractions on Type 2 Diabetes and Its Complications
Cited by: 35
Author(s): Ochuko L. Erukainure, Rahman M. Hafizur, Nurul Kabir, M. Iqbal Choudhary, Olubunmi Atolanı, Priyanka Banerjee, Robert Preißner, Chika I. Chukwuma, Aliyu Muhammad, Eric O. Amonsou, Md. Shahidul Islam
Software Mentions: 2
Published: almost 8 years ago

10.3390/molecules25040823

Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies
Cited by: 76
Author(s): Taj Mohammad, Shiza Siddiqui, Anas Shamsi, Mohamed F. Alajmi, Afzal Hussain, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.RA120.015376

Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes
Cited by: 4
Author(s): Sebastián M. Muñoz, Víctor Castro‐Fernández, Victoria Guixé
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0105984

Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries
Cited by: 46
Author(s): Olivier Barré, Antoine Dufour, Ulrich Eckhard, Reinhild Kappelhoff, François Béliveau, Richard Leduc, Christopher M. Overall
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1005895

Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer
Cited by: 138
Author(s): Liyan Jiang, Jiaqi Huang, Brandon W. Higgs, Zhibin Hu, Xiaowei Zhan, Xin Yao, R. Scott Conley, Haihong Zhong, Zheng Liu, Philip Z. Brohawn, Dong Shen, Song Wu, Xiaoxiao Ge, Yue Jiang, Yupei Zhao, Yu‐Qing Lou, Chris Morehouse, Wei Zhu, Yinong Sebastian, Meggan Czapiga, Vaheh Oganesyan, Haihua Fu, Yiming Niu, Wei Zhang, Katie Streicher, David A. Tice, Heng Zhao, Meng Zhu, Lin Xu, Ronald Herbst, Xinying Su, Yi Gu, Shyoung Li, Lihua Huang, Jianren Gu, Baohui Han, Bahija Jallal, Hongbing Shen, Yihong Yao
Software Mentions: 2
Published: over 9 years ago

10.3389/fonc.2021.606820

Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level
Cited by: 3
Author(s): Michael T. Zimmermann, Angela Mathison, Tim Stodola, Douglas B. Evans, Jenica Abrudan, Wendy Demos, Michael Tschannen, Mohammed Aldakkak, Jennifer L. Geurts, Gwen Lomberk, Susan Tsai, Raúl Urrutia
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0167755

Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A
Cited by: 10
Author(s): Jonathan Gaucher, Marie Reille‐Seroussi, Nathalie Gagey‐Eilstein, Sylvain Broussy, Pascale Coric, Bili Seijo, Marie-Bernard Lascombe, Benoît Gautier, Wang-Quing Liu, Florent Huguenot, Nicolas Inguimbert, Serge Bouaziz, Michel Vidal, Isabelle Broutin
Software Mentions: 2
Published: almost 9 years ago

10.3389/fonc.2019.01294

p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma
Cited by: 19
Author(s): Ling Yang, Xiaoting Sun, Ying Ye, Yongtian Lu, Jiane Zuo, Wen Li, Adrian H. Elcock, Shun Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1006959

Ten quick tips for using a Raspberry Pi
Cited by: 10
Author(s): Anthony C. Fletcher, Cameron Mura
Software Mentions: 2
Published: over 6 years ago

10.3389/fphar.2019.00474

Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors
Cited by: 38
Author(s): Marios Zouridakis, Athanasios Papakyriakou, Igor A. Ivanov, Igor E. Kasheverov, Victor I. Tsetlin, Socrates J. Tzartos, Petros Giastas
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0216979

Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis
Cited by: 2
Author(s): Ke Shi, Chong-Min Kyung, Kelly G. Aukema, Thomas Lee, Asim K. Bera, Jennifer L. Seffernick, Lawrence P. Wackett, Hideki Aihara
Software Mentions: 2
Published: over 6 years ago

10.1074/jbc.M114.624650

Vaccinia Virus Protein A49 Is an Unexpected Member of the B-cell Lymphoma (Bcl)-2 Protein Family
Cited by: 51
Author(s): Sarah Neidel, Carlos Maluquer de Motes, Daniel Santos Mansur, Pavla Strnadova, Geoffrey L. Smith, Stephen C. Graham
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1004620

NMR Methods to Study Dynamic Allostery
Cited by: 58
Author(s): Sarina Grutsch, Sven Brüschweiler, Martin Tollinger
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0050769

Using RosettaLigand for Small Molecule Docking into Comparative Models
Cited by: 38
Author(s): Kristian Kaufmann, Jens Meiler
Software Mentions: 2
Published: almost 13 years ago

10.3389/fmolb.2015.00056

A script to highlight hydrophobicity and charge on protein surfaces
Cited by: 83
Author(s): Dominique Hagemans, Ianthe A. E. M. van Belzen, Tania Morán Luengo, Stefan Rüdiger
Software Mentions: 2
Published: about 10 years ago

10.3389/fnmol.2014.00051

In silico, in vitro and cellular analysis with a kinome-wide inhibitor panel correlates cellular LRRK2 dephosphorylation to inhibitor activity on LRRK2
Cited by: 46
Author(s): Renée Vancraenenbroeck, Joren De Raeymaecker, Evy Lobbestael, Fangye Gao, Marc De Maeyer, Arnout Voet, Veerle Baekelandt, Jean-Marc Taymans
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002484

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
Cited by: 22
Author(s): Takehiro Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski
Software Mentions: 2
Published: almost 14 years ago

10.3389/fmolb.2020.00029

Molecular Simulation of Oncostatin M and Receptor (OSM–OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease
Cited by: 19
Author(s): Qingqing Du, Qian Yan, Weiwei Xue
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-016-0605-z

Structural and functional characterization of a highly stable endo-β-1,4-xylanase from Fusarium oxysporum and its development as an efficient immobilized biocatalyst
Cited by: 18
Author(s): Sara Gómez, Asia M. Payne, Martin Savko, Gavin C. Fox, William Shepard, Francisco Fernández, M. Cristina Vega
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1003103

The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove
Cited by: 84
Author(s): Minzhong Tang, James A. Lautenberger, Xiaojiang Gao, Efe Sezgın, Sher L. Hendrickson, Jennifer L. Troyer, Victor A. David, Li Guan, Carl McIntosh, Xiuchan Guo, Yuming Zheng, Jian Liao, Hong Wen Deng, Michael Malasky, Bailey Kessing, Cheryl A. Winkler, Mary Carrington, Yi Zeng, Stephen J. O’Brien
Software Mentions: 2
Published: almost 13 years ago

10.3389/fmolb.2017.00068

Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp
Cited by: 18
Author(s): E. Krysztofinska, N.J. Evans, Arjun Thapaliya, James W. Murray, Rhodri M. L. Morgan, Santiago Martínez-Lumbreras, Rivka L. Isaacson
Software Mentions: 2
Published: about 8 years ago

10.3389/fnmol.2018.00113

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate
Cited by: 24
Author(s): Marek Ladislav, Jiří Černý, Jan Krůšek, Martin Hořák, Aleš Balík, Ladislav Vyklicky
Software Mentions: 2
Published: over 7 years ago

10.3389/fmolb.2021.642606

Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICESt3 From Streptococcus thermophilus
Cited by: 2
Author(s): Julien Cappele, Abbas M. Ali, Nathalie Leblond‐Bourget, Sandrine Mathiot, Tiphaine Dhalleine, Sophie Payot, Martin Savko, Claude Didierjean, F. Favier, Badreddine Douzi
Software Mentions: 2
Published: over 4 years ago

10.3389/fmolb.2021.614443

Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation
Cited by: 5
Author(s): Yaoqiang Du, Hao Wang, Linjie Chen, Quan Fang, Biqin Zhang, Jiang Lei, Zhaoyu Wu, Yuanhong Yang, Ying Zhou, Bingyu Chen, Jianxin Lyu, Zhen Wang
Software Mentions: 2
Published: over 4 years ago

10.1016/j.bpj.2015.02.013

Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation
Cited by: 71
Author(s): Sonya M. Hanson, Simon Newstead, Kenton J. Swartz, Mark S.P. Sansom
Software Mentions: 2
Published: over 10 years ago

10.3389/fmolb.2019.00041

Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome
Cited by: 48
Author(s): Mohd. Amir, Taj Mohammad, Vijay Kumar, Mohamed F. Alajmi, Tabish Rehman, Afzal Hussain, Perwez Alam, Ravins Dohare, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0201556

Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Cited by: 16
Author(s): Noah Machuki Onchieku, Reagan M. Mogire, Loise Ndung’u, Peter Mwitari, Francis Kimani, Damaris Matoke-Muhia, Daniel Kiboi, Gabriel Magoma
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005824

Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis
Cited by: 94
Author(s): Pablo Pulido, Ernesto Llamas, Briardo Llorente, Salvador Ventura, Louwrance P. Wright, Manuel Rodrı́guez-Concepción
Software Mentions: 2
Published: almost 10 years ago

10.1074/jbc.M115.669895

Structural Basis for Antigen Recognition by Transglutaminase 2-specific Autoantibodies in Celiac Disease
Cited by: 27
Author(s): Xi Chen, Kathrin Hnida, Melissa A. Graewert, Jan Terje Andersen, Rasmus Iversen, Anne Tuukkanen, Dmitri I. Svergun, Ludvig M. Sollid
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2020.598692

Bacterial ClpP Protease Is a Potential Target for Methyl Gallate
Cited by: 6
Author(s): Danxing Zheng, Yanan Xu, Gonglin Yuan, Xiaogang Wu, Qiqin Li
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmolb.2021.724947

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction
Cited by: 16
Author(s): Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara
Software Mentions: 2
Published: over 4 years ago

10.3389/fmolb.2021.644720

A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism
Cited by: 3
Author(s): Alessandro Crnjar, Susanne M. Mesoy, Sarah C. R. Lummis, Carla Molteni
Software Mentions: 2
Published: over 4 years ago

10.1074/jbc.M113.523019

Affinity Map of Bromodomain Protein 4 (BRD4) Interactions with the Histone H4 Tail and the Small Molecule Inhibitor JQ1
Cited by: 118
Author(s): Marie Jung, Martin Philpott, Susanne Müller, Jessica Schulze, Volker Badock, Uwe Eberspächer, Dieter Moosmayer, Benjamin Bader, Norbert Schmees, Amaury E. Fernández-Montalván, Bernard Haendler
Software Mentions: 2
Published: over 11 years ago

10.3389/fnmol.2018.00330

Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction
Cited by: 9
Author(s): Anne Rehkamp, Dirk Tänzler, Claudio Iacobucci, Ralph Golbik, Christian Ihling, Andrea Sinz
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0042473

Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains
Cited by: 51
Author(s): Federico Carafoli, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1004130

Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
Cited by: 62
Author(s): Juan Manuel Palacios‐Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael J. Comb, Mark L. Grimes
Software Mentions: 2
Published: over 10 years ago

10.3389/fphar.2015.00017

Optimization of the cyclotide framework to improve cell penetration properties
Cited by: 26
Author(s): Yen‐Hua Huang, Stephanie Chaousis, Olivier Cheneval, David J. Craik, Sónia Troeira Henriques
Software Mentions: 2
Published: almost 11 years ago

10.3389/fmicb.2020.01501

Influence of Catecholamines (Epinephrine/Norepinephrine) on Biofilm Formation and Adhesion in Pathogenic and Probiotic Strains of Enterococcus faecalis
Cited by: 26
Author(s): Mélyssa Cambronel, Flore Nilly, Ouiza Mesguida, Amine M. Boukerb, Pierre‐Jean Racine, Olfa Baccouri, Valérie Borrel, J Forga Martel, Florian Fécamp, Rikki Knowlton, Kurt Zimmermann, Eugen Domann, Sophie Rodrigues, Marc Feuilloley, Nathalie Connil
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.02755

Characterization of a Dimeric Arginase From Zymomonas mobilis ZM4
Cited by: 6
Author(s): Seung-A Hwangbo, Jiwon Kim, Sun-Ju Jung, Kyeong Sik Jin, Jie‐Oh Lee, Ji Soo Kim, Suk-Youl Park
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1002326

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Cited by: 59
Author(s): Tianyun Liu, Russ B. Altman
Software Mentions: 2
Published: almost 14 years ago

10.3389/fmicb.2019.01151

Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses
Cited by: 31
Author(s): Xi Liu, Heng Zheng, Rigang Lu, Huimin Huang, Hongjia Zhu, Chunli Yin, Yi-Yi Mo, Jinxia Wu, Xuwen Liu, Ming Deng, Danfeng Li, Bang Cheng, Fang Wu, Yonghong Liu, Hongwei Guo, Hui Song, Zhiheng Su
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.01226

Regulation of Exopolysaccharide Production by ProE, a Cyclic-Di-GMP Phosphodiesterase in Pseudomonas aeruginosa PAO1
Cited by: 17
Author(s): Qiang Feng, Stephen Dela Ahator, Tianxing Zhou, Zhiqing Liu, Qiqi Lin, Yang Liu, Jiahui Huang, Jianuan Zhou, Lian-Hui Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.633489

Gene Expression, Biochemical Characterization of a sn-1, 3 Extracellular Lipase From Aspergillus niger GZUF36 and Its Model-Structure Analysis
Cited by: 4
Author(s): Shuqi Xing, Ruonan Zhu, Kai Cheng, Yangyang Cai, Yuedan Hu, Cuiqin Li, Xuefeng Zeng, Qiujin Zhu, Laping He
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2018.02536

The GbsR Family of Transcriptional Regulators: Functional Characterization of the OpuAR Repressor
Cited by: 5
Author(s): Stefanie Ronzheimer, Bianca Warmbold, Christian Arnhold, Erhard Bremer
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0195355

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation
Cited by: 1
Author(s): Jumei Zeng, Yipeng Jin, Zhongchuan Liu
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2020.01529

The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage
Cited by: 11
Author(s): Jeffrey Zhou, Hussain Zaidi, Therese Ton, Daniela Fera
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2018.03102

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

10.3389/fimmu.2021.621153

Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First
Cited by: 16
Author(s): Yanan Wu, Nianzhi Zhang, Keiichiro Hashimoto, Chun Xia, Johannes M. Dijkstra
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0107000

Crystal Structure of the Mineralocorticoid Receptor DNA Binding Domain in Complex with DNA
Cited by: 39
Author(s): William Henry Hudson, Christine Youn, Eric A. Ortlund
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0052066

Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase, a Metabolic Branch Point Enzyme in Nitrogen Utilization
Cited by: 4
Author(s): Myungil Kim, Inchul Shin, Suhee Cho, Jee Hyun Lee, Sangkee Rhee
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0123996

Novel Non-Peptide Inhibitors against SmCL1 of Schistosoma mansoni: In Silico Elucidation, Implications and Evaluation via Knowledge Based Drug Discovery
Cited by: 5
Author(s): Atif Zafar, Sameena Ahmad, Asim Rizvi, Masood Ahmad
Software Mentions: 2
Published: over 10 years ago

10.3389/fimmu.2021.592447

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

10.1371/journal.pgen.1005569

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

10.3389/fimmu.2021.639489

Transcriptional Profiles of Genes Related to Stress and Immune Response in Rainbow Trout (Oncorhynchus mykiss) Symptomatically or Asymptomatically Infected With Vibrio anguillarum
Cited by: 8
Author(s): Zhi-Shuai Hou, Yuan-Ru Xin, Xiaodong Yang, Chu Zeng, Hong-Kui Zhao, Meng-Qun Liu, Mei-Zhao Zhang, Jeffrey G. Daniel, Jifang Li, Haishen Wen
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.620494

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

10.3389/fmicb.2020.01178

Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans
Cited by: 6
Author(s): Yuan He, Yiyi Wang, Qin Chen, Ying Xu, Kaiying Cheng, Hong Xu, Bing Teng, Ye Zhao, Liangyan Wang, Yuejin Hua
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M117.802587

Phosphorylation of human enhancer filamentation 1 (HEF1) stimulates interaction with Polo-like kinase 1 leading to HEF1 localization to focal adhesions
Cited by: 6
Author(s): Kyung Ho Lee, Jeong Ah Hwang, Sun Ok Kim, Jung Hee Kim, Sang Chul Shin, Eunice Eun Kyeong Kim, Kyung S. Lee, Kunsoo Rhee, Byeong Hwa Jeon, Jeong Kyu Bang, Hyunjoo Cha-Molstad, Nak-Kyun Soung, Jae Hyuk Jang, Sung-Kyun Ko, Hee Gu Lee, Jong Seog Ahn, Yongtae Kwon, Bo Yeon Kim
Software Mentions: 2
Published: almost 8 years ago

10.1093/protein/gzx044

Novel CH1:CL interfaces that enhance correct light chain pairing in heterodimeric bispecific antibodies
Cited by: 26
Author(s): Maximilian Bönisch, Carolin Sellmann, Daniel Maresch, Claudia Halbig, Stefan Becker, Lars Toleikis, Björn Hock, Florian Rüker
Software Mentions: 2
Published: about 8 years ago

10.1016/j.str.2016.10.005

Functional Annotation of Ion Channel Structures by Molecular Simulation
Cited by: 60
Author(s): Jemma L. Trick, Sivapalan Chelvaniththilan, Gianni Klesse, Prafulla Aryal, E. Jayne Wallace, Stephen J. Tucker, Mark S. P. Sansom
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-014-0434-7

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions
Cited by: 3
Author(s): Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew Yeh, Adam Godzik, L. Aravind
Software Mentions: 2
Published: almost 11 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

10.3390/biom10010046

Identification of the NADP+ Structural Binding Site and Coenzyme Effect on the Fused G6PD::6PGL Protein from Giardia lamblia
Cited by: 6
Author(s): Laura Morales-Luna, Abigail González‐Valdez, Yudibeth Sixto‐López, José Correa‐Basurto, Beatriz Hernández-Ochoa, Noemí Cárdenas-Rodríguez, Rosa Angélica Castillo-Rodríguez, Daniel Ortega-Cuéllar, Roberto Arreguı́n-Espinosa, Verónica Pérez de la Cruz, Hugo Serrano‐Posada, Sara Centeno-Leija, Luz María Rocha-Ramírez, Edgar Sierra-Palacios, Alba Mónica Montiel-González, Yadira Rufino-González, Jaime Marcial-Quino, Saúl Gómez-Manzo
Software Mentions: 2
Published: almost 6 years ago

10.1107/S1399004714001308

Automated identification of elemental ions in macromolecular crystal structures
Cited by: 37
Author(s): Nathaniel Echols, Nader Morshed, Pavel V. Afonine, Airlie J. McCoy, Mitchell D. Miller, Randy J. Read, Jane S. Richardson, Thomas C. Terwilliger, Paul D. Adams
Software Mentions: 2
Published: over 11 years ago

10.1107/S2053230X14003355

A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
Cited by: 13
Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: over 11 years ago

10.1107/S2053230X14017087

Structure of<i>Toxoplasma gondii</i>fructose-1,6-bisphosphate aldolase
Cited by: 8
Author(s): Lauren Boucher, Jürgen Bosch
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-12-313

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database
Cited by: 56
Author(s): G. Richard J. Bickerton, Alícia P. Higueruelo, Tom L. Blundell
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0011092

Modelling the Response of FOXO Transcription Factors to Multiple Post-Translational Modifications Made by Ageing-Related Signalling Pathways
Cited by: 35
Author(s): Graham R. Smith, Daryl P. Shanley
Software Mentions: 2
Published: over 15 years ago

10.1107/S2053230X18002236

Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis
Cited by: 1
Author(s): Adarsh Kumar, Subramanian Karthikeyan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12915-021-01039-8

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors
Cited by: 30
Author(s): Yoshihisa Hirakawa, Masuo Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, M. Taira, Kazushi Kinbara, Toshiya Senda
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0210842

Potent, multi-target serine protease inhibition achieved by a simplified β-sheet motif
Cited by: 7
Author(s): Xingchen Chen, Blake T. Riley, Simon J. de Veer, David E. Hoke, Jessica Van Haeften, Darren Leahy, Joakim E. Swedberg, Maria Brattsand, Perry J. Hartfield, Ashley M. Buckle, Jonathan M. Harris
Software Mentions: 2
Published: almost 7 years ago

10.1107/S2053230X19012172

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
Cited by: 3
Author(s): Eric Montemayor, Johanna M Virta, Lauren D. Hagler, Steven C. Zimmerman, Samuel E. Butcher
Software Mentions: 2
Published: about 6 years ago

10.6026/97320630013086

Epitope design of L1 protein for vaccine production against Human Papilloma Virus types 16 and 18
Cited by: 8
Author(s): Sunanda Baidya, Rasel Das, Md. Golam Kabir, Md. Arifuzzaman
Software Mentions: 2
Published: over 8 years ago

10.3390/biom11081251

Computational Insights into the Structural Dynamics of MDA5 Variants Associated with Aicardi–Goutières Syndrome and Singleton–Merten Syndrome
Cited by: 12
Author(s): Vijayakumar Gosu, Santanu Sasidharan, Prakash Saudagar, Hak-Kyo Lee, Donghyun Shin
Software Mentions: 2
Published: about 4 years ago

10.1186/s12915-015-0167-8

Role of electrostatic interactions for ligand recognition and specificity of peptide transporters
Cited by: 47
Author(s): Rajendra Boggavarapu, Jean-Marc Jeckelmann, Daniel Harder, Zöhre Ucurum, Dimitrios Fotiadis
Software Mentions: 2
Published: over 10 years ago

10.6026/97320630017337

Differential binding of SARS-CoV-2 Spike protein variants to its cognate receptor hACE2 using molecular modeling based binding analysis
Cited by: 2
Author(s): Anuja Krishnan
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0227287

Two novel mutations in MSX1 causing oligodontia
Cited by: 5
Author(s): Yang Le, Jia Liang, Haitang Yue, Zhuan Bian
Software Mentions: 2
Published: almost 6 years ago

10.1107/S2053230X18006519

Crystal structure of an inactive variant of the quorum-sensing master regulator HapR from the protease-deficient non-O1, non-O139<i>Vibrio cholerae</i>strain V2
Cited by: 7
Author(s): Justin T. Cruite, Patrick Succo, Saumya Raychaudhuri, F. Jon Kull
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0223464

Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
Cited by: 15
Author(s): Rumbidzai Chitongo, Adetayo Emmanuel Obasa, Sello Given Mikasi, Graeme Brendon Jacobs, Ruben Cloete
Software Mentions: 2
Published: over 5 years ago

10.3390/biom11040573

Molecular Simulation-Based Investigation of Highly Potent Natural Products to Abrogate Formation of the nsp10–nsp16 Complex of SARS-CoV-2
Cited by: 12
Author(s): Anwar Mohammad, Eman Alshawaf, Sulaiman K. Marafie, Mohamed Abu‐Farha, Fahd Al-Mulla, Jehad Abubaker
Software Mentions: 2
Published: over 4 years ago

10.3390/biom10081166

Discovery of Sulfated Small Molecule Inhibitors of Matrix Metalloproteinase-8
Cited by: 8
Author(s): Shravan Morla, Umesh R. Desai
Software Mentions: 2
Published: over 5 years ago

10.3390/biom11070935

The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex
Cited by: 4
Author(s): Urszula Orzeł, Jakub Jakowiecki, Krzysztof Młynarczyk, Sławomir Filipek
Software Mentions: 2
Published: over 4 years ago

10.1107/S2053230X16007263

Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from<i>Arabidopsis thaliana</i>
Cited by: 7
Author(s): Youhong Song, Hua Pu, Tianyue Jiang, Lixin Zhang, Ming Ouyang
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2091-12-12

The Peroxisomal Targeting Signal 1 in sterol carrier protein 2 is autonomous and essential for receptor recognition
Cited by: 9
Author(s): Chris Williams, Nicole Schueller, Colin A. Thompson, Marlene van den Berg, Simon D. van Haren, Ralf Erdmann, Charles S. Bond, Ben Distel, Wolfgang Schliebs, Matthias Wilmanns, Will A. Stanley
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0239702

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

10.1186/s13628-018-0048-y

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

10.1016/j.bbapap.2017.08.005

Thermal sensitivity and flexibility of the Cε3 domains in immunoglobulin E
Cited by: 9
Author(s): K.A. Dore, Anna M. Davies, N. Drinkwater, Andrew J. Beavil, James M. McDonnell, Brian J. Sutton
Software Mentions: 2
Published: about 8 years ago

10.1107/S0907444911007888

Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis
Cited by: 27
Author(s): Róisín M. McMahon, Lone Smidstrup Friis, Christian Siebold, Manuel A. Friese, Lars Fugger, E Y Jones
Software Mentions: 2
Published: over 14 years ago

10.1186/1472-6750-11-85

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
Cited by: 36
Author(s): Gustavo R. Oliveira, Maria C. M. Silva, Wagner Alexandre Lucena, Erich Yukio Tempel Nakasu, Alexandre Augusto Pereira Firmino, Magda Aparecida Beneventi, Djair S.L. Souza, José Erick Galindo Gomes, José Dijair Antonino, Daniel J. Rigden, H. B. Ramos, Carlos Ricardo Soccol, Maria Fátima Grossi‐de‐Sá
Software Mentions: 2
Published: about 14 years ago

10.3390/biom9110723

The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin
Cited by: 8
Author(s): Andrés Vacas, Celia Fernández-Rubio, Miriam Algarabel, José Peña-Guerrero, Esther Larrea, Fabio Rocha Formiga, Alfonso T. García-Sosa, Paul A. Nguewa
Software Mentions: 2
Published: about 6 years ago

10.3390/biom11010043

On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme
Cited by: 3
Author(s): Lucia Gigli, Enrico Ravera, V. Calderone, Claudio Luchinat
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0043985

Stapled BH3 Peptides against MCL-1: Mechanism and Design Using Atomistic Simulations
Cited by: 37
Author(s): Thomas L. Joseph, David P. Lane, Chandra Verma
Software Mentions: 2
Published: about 13 years ago