Ecosyste.ms: Papers

10.1107/S2052252517008557

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Cited by: 22
Author(s): Keitaro Yamashita, N. Kuwabara, Takanori Nakane, Taichi Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Satō, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Katô, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu
Software Mentions: 4
Published: almost 7 years ago

10.1007/s10822-017-0049-y

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Cited by: 94
Author(s): Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikaël Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel‐Touris, Adrien Melquiond, Cunliang Geng, Jörg Schaarschmidt, Xue Li, Anna Vangone, Alexandre M. J. J. Bonvin
Software Mentions: 4
Published: over 6 years ago

10.1126/sciadv.aax8286

Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity
Cited by: 53
Author(s): Ni Tien, Fang Jiao, Xiulian Yu, Saša Aden, Lucy Ginger, Sophie I. Williams, Fangfang Bai, Vojtěch Pražák, Dimple Karia, Phillip J. Stansfeld, Peijun Zhang, George P. Munson, Gregor Anderluh, Simon Scheuring, R.J.C. Gilbert
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-52825-y

A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser
Cited by: 2
Author(s): Si Hoon Park, Jaehyun Park, Sang Jae Lee, Woo Seok Yang, Sehan Park, Kyungdo Kim, Zee Yong Park, Hyun Kyu Song
Software Mentions: 3
Published: over 4 years ago

10.15252/msb.20209840

From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration
Cited by: 7
Author(s): Maria Palafox, Heta S Desai, Valerie A. Arboleda, Keriann M. Backus
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-46756-x

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India
Cited by: 31
Author(s): Asma Munir, Narender Kumar, Suresh Babu Ramalingam, Sembulingam Tamilzhalagan, Siva Kumar Shanmugam, Alangudi Natarajan Palaniappan, Dina Nair, Padma Priyadarshini, Mohan Natarajan, Srikanth Tripathy, Uma Devi Ranganathan, Sharon J. Peacock, Julian Parkhill, Tom L. Blundell, Sony Malhotra
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0248887

Production and characterization of antibody against Opisthorchis viverrini via phage display and molecular simulation
Cited by: 0
Author(s): Sitthinon Siripanthong, Anchalee Techasen, Chanin Nantasenamat, Aijaz Ahmad Malik, Paiboon Sithithaworn, Chanvit Leelayuwat, Amonrat Jumnainsong
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2018.03192

Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1
Cited by: 29
Author(s): Stephen Wandro, Andrew Oliver, Tara Gallagher, Claudia Weihe, Whitney England, Jennifer B. H. Martiny, Katrine Whiteson
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.03549-20

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator
Cited by: 23
Author(s): Shruti Nagaraja, Maggi W. Cai, Jingjing Sun, Hugo Varet, Lotem Sarid, Meirav Trebicz-Geffen, Yana Shaulov, Mohit Mazumdar, Rachel Legendre, Jean‐Yves Coppée, Thomas J. Begley, Peter C. Dedon, S. Gourinath, Nancy Guillén, Yumiko Saito‐Nakano, Chikako Shimokawa, Hajime Hisaeda, Serge Ankri
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0169687

Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO)
Cited by: 59
Author(s): Allison Cox, Benjamin W. Darbro, Ronald M. Laxer, Gabriel Vélez, Xinyu Bing, Alexis L. Finer, Albert Erives, Vinit B. Mahajan, Alexander G. Bassuk, Polly J. Ferguson
Software Mentions: 3
Published: about 7 years ago

10.26508/lsa.202101152

The structure and flexibility analysis of the <i>Arabidopsis</i> synaptotagmin 1 reveal the basis of its regulation at membrane contact sites
Cited by: 8
Author(s): Juan Luis Benavente, Dritan Siliqi, Lourdes Infantes, Laura Lagartera, Alberto Mills, Federico Gago, Noemı́ Ruiz-López, Miguel A. Botella, María José Sánchez-Barrena, Armando Albert
Software Mentions: 3
Published: almost 3 years ago

10.1016/j.cell.2018.11.025

The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier
Cited by: 206
Author(s): Jonathan J. Ruprecht, Martin King, Thomas Zögg, Antoniya A. Aleksandrova, Els Pardon, Paul G. Crichton, Jan Steyaert, Edmund R. S. Kunji
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2016.01810

The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles
Cited by: 9
Author(s): Marcela Iara Rodrigues, Agnes Alessandra Sekijima Takeda, Juliana Pereira Bravo, Ivan de Godoy Maia
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers13143418

Phosphorylation of OGFOD1 by Cell Cycle-Dependent Kinase 7/9 Enhances the Transcriptional Activity of RNA Polymerase II in Breast Cancer Cells
Cited by: 1
Author(s): Han Teo Lee, Il Hwan Lee, Jaehwan Kim, Sang-Ho Lee, Sojung Kwak, Min Young Suh, In Kyeom Hwang, Bu Gyeong Kang, Sun Shin, Byung Il Lee, Sang Eun Lee, Jinmi Choi, Jae Seok Roe, Eun Jung Cho, Hong Duk Youn
Software Mentions: 3
Published: almost 3 years ago

10.3389/fmolb.2021.643728

Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction
Cited by: 1
Author(s): Ennys Gheyouche, Matthias Bagueneau, Gervaise Loirand, Bernard Offmann, Stéphane Téletchéa
Software Mentions: 3
Published: almost 3 years ago

10.3390/md16100386

Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer’s Disease: A Computational Study
Cited by: 25
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Conxita Àvila, Melchor Sánchez-Martínez
Software Mentions: 3
Published: over 5 years ago

10.15252/emmm.201911210

Glufosinate constrains synchronous and metachronous metastasis by promoting anti‐tumor macrophages
Cited by: 27
Author(s): Alessio Menga, Marina Serra, Simona Todisco, Carla Riera-Domingo, Ummi Ammarah, Manuel Ehling, Erika M. Palmieri, Maria Antonietta Di Noia, Rosanna Gissi, Maria Favia, Ciro Leonardo Pierri, Paolo E. Porporato, Alessandra Castegna, Massimiliano Mazzone
Software Mentions: 3
Published: over 3 years ago

10.1038/s41421-020-00215-4

A novel multistage antiplasmodial inhibitor targeting Plasmodium falciparum histone deacetylase 1
Cited by: 20
Author(s): Zhenghui Huang, Ruoxi Li, Tongke Tang, Dazheng Ling, Manjiong Wang, Dandan Xu, Maoxin Sun, Lulu Zheng, Feng Zhu, Hui Min, Rachasak Boonhok, Yan Ding, Yang Wen, Zhong Chen, Xiaokang Li, Yuxi Chen, Taiping Liu, Jiping Han, Jun Miao, Qiang Fang, Yaming Cao, Yun Tang, Jie Cui, Wei Xu, Liwang Cui, Jin Zhu, Gary Wong, Jian Li, Lubin Jiang
Software Mentions: 3
Published: over 3 years ago

10.3390/life5021264

The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets
Cited by: 14
Author(s): Birgit Märtens, G.A. Bezerra, Mathias Josef Kreuter, Irina Grishkovskaya, Andrea Manica, Valentina Arkhipova, Kristina Djinović-Carugo, Udo Bläsi
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms20040884

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies
Cited by: 67
Author(s): Shahid Ali, Faez Iqbal Khan, Taj Mohammad, Dongming Lan, Md. Imtaiyaz Hassan, Yonghua Wang
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00416-19

Genomewide Analysis of Mode of Action of the <i>S</i> -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Cited by: 13
Author(s): Arijit Bhattacharya, Meenakshi Sharma, Charles Packianathan, Barry P. Rosen, Philippe Leprohon, Marc Ouellette
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0167978

Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases
Cited by: 12
Author(s): Fábio K. Tamaki, Diorge P. Souza, Valquiria P. Souza, Cecília M. Ikegami, Chuck S. Farah, Sandro R. Marana
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.00070

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase
Cited by: 6
Author(s): Seon‐Kap Hwang, S. S. Singh, Jitendra Maharana, S. N. Kalita, Aytuğ Tuncel, Tanmayee Rath, Debashis Panda, Mahendra Kumar Modi, Thomas W. Okita
Software Mentions: 3
Published: over 5 years ago

10.1038/celldisc.2016.51

Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway
Cited by: 33
Author(s): Zhongchao Gai, Qian Wang, Can Yang, Lei Wang, Wei Deng, Geng Wu
Software Mentions: 3
Published: over 7 years ago

10.1016/j.cell.2021.02.045

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: about 3 years ago

10.1155/2021/6696012

Active Learning and the Potential of Neural Networks Accelerate Molecular Screening for the Design of a New Molecule Effective against SARS-CoV-2
Cited by: 3
Author(s): Yassine Rabhi, Makrem Mrabet, Farhat Fnaiech
Software Mentions: 3
Published: almost 3 years ago

10.15252/emmm.201911592

STIM1‐mediated calcium influx controls antifungal immunity and the metabolic function of non‐pathogenic Th17 cells
Cited by: 22
Author(s): Sascha Kahlfuß, Ulrike Kaufmann, Axel R. Concepcion, Lucile Noyer, Dimitrius Raphael, Martin Vaeth, Jun J. Yang, Priya Pancholi, Máté Maus, James Muller, Lina Kozhaya, Alireza Khodadadi‐Jamayran, Zhengxi Sun, Patrick J. Shaw, Derya Unutmaz, Peter B. Stathopulos, Cori Feist, Scott Cameron, Stuart E. Turvey, Stefan Feske
Software Mentions: 3
Published: almost 4 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.01100

Characterization of a Novel Functional Trimeric Catechol 1,2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico
Cited by: 16
Author(s): Julieta Rodríguez-Salazar, Arisbeth G Almeida-Juarez, Katya Ornelas-Ocampo, Sofía Millán-López, Enrique Raga-Carbajal, José Luis Rodríguez-Mejía, Luis Felipe Muriel-Millán, Elizabeth Ernestina Godoy-Lozano, Nancy Rivera-Gómez, E. Rudiño-Piñera, Liliana Pardo-López
Software Mentions: 3
Published: almost 4 years ago

10.3390/medsci7060074

In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts
Cited by: 0
Author(s): P. Sneha, Urmi Shah, S. Balaji
Software Mentions: 3
Published: almost 5 years ago

10.1155/2013/185282

Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein
Cited by: 20
Author(s): Bikash R. Sahoo, Madhubanti Basu, Bichitrananda Swain, Manas Ranjan Dikhit, P. Jayasankar, Mrinal Samanta
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2016.00901

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae
Cited by: 8
Author(s): Tilen Konte, Ulrich Terpitz, Ana Plemenitaš
Software Mentions: 3
Published: almost 8 years ago

10.15252/embj.2021107985

Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies
Cited by: 56
Author(s): Thomas Güttler, Metin Aksu, Antje Dickmanns, Kim M. Stegmann, Kathrin Gregor, Renate Rees, Waltraud Taxer, Oleh Rymarenko, Jürgen Schünemann, Christian Dienemann, Philip Gunkel, Bianka Mußil, Jens Krull, Ulrike Teichmann, Uwe Groß, Volker C. Cordes, Matthias Dobbelstein, Dirk Görlich
Software Mentions: 3
Published: almost 3 years ago

10.3389/frobt.2018.00133

Authenticity, Interactivity, and Collaboration in VR Learning Games
Cited by: 9
Author(s): Meredith Thompson, Annie Wang, Dan Roy, Eric Klopfer
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13071618

Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells
Cited by: 10
Author(s): Emilie Logie, Chandra Sekhar Chirumamilla, Claudina Pérez-Novo, Priyanka Shaw, Ken Declerck, Ajay Palagani, Savithri Rangarajan, Bart Cuypers, Nicolas De Neuter, Mobashar Hussain Urf Turabe Fazil, Navin Kumar Verma, Annemie Bogaerts, Kris Laukens, Fritz Offner, Pieter Van Vlierberghe, Xaveer Van Ostade, Wim Vanden Berghe
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0145053

Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans
Cited by: 57
Author(s): Aijaz Ahmad, Mohmmad Younus Wani, Amber Khan, Nikhat Manzoor, Julitha Molepo
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-48849-z

Modelling of substrate access and substrate binding to cephalosporin acylases
Cited by: 6
Author(s): Virgilio F. Ferrario, Mona Fischer, Yushan Zhu, Jürgen Pleiss
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0182016

An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins
Cited by: 20
Author(s): Marcin Michalik, Marcella Orwick‐Rydmark, Michael Habeck, Vikram Alva, Thomas C. Arnold, Dirk Linke
Software Mentions: 3
Published: almost 7 years ago

10.1042/BJ20141324

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases
Cited by: 61
Author(s): Karen McLuskey, Jeremy C. Mottram
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0121415

Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Docking and Molecular Dynamics Simulations
Cited by: 31
Author(s): Jitendra Maharana, Bikash R. Sahoo, Aritra Bej, Itishree Jena, Arunima Parida, Jyoti Ranjan Sahoo, Budheswar Dehury, Mahesh Chandra Patra, Sushma Rani Martha, Sucharita Balabantray, Sukanta Kumar Pradhan, Bijay Kumar Behera
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0241513

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX
Cited by: 12
Author(s): Linda Yingqi Lin, Sawyer McCarthy, Barrett M. Powell, Yanti Manurung, Irene M. Xiang, William L. Dean, Brad Chaires, Liliya A. Yatsunyk
Software Mentions: 3
Published: over 3 years ago

10.3390/v12010105

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111
Cited by: 8
Author(s): Aaron E. Lin, William E. Diehl, Yíngyún Caì, Courtney Finch, Chidiebere Akusobi, Robert N. Kirchdoerfer, Laura Bollinger, Stephen F. Schaffner, Elizabeth Brown, Erica Ollmann Saphire, Kristian G. Andersen, Jens H. Kuhn, Jeremy Luban, Pardis C. Sabeti
Software Mentions: 3
Published: over 4 years ago

10.3390/v11020167

Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus
Cited by: 25
Author(s): Wenyan Zhang, Letian Zhang, Wanting He, Xu Zhang, Baiqing Wen, Congcong Wang, Qiuhua Xu, Gairu Li, Jiyong Zhou, Michael Veit, Shuo Su
Software Mentions: 3
Published: about 5 years ago

10.1128/mSphere.00454-21

A Novel Phage Infecting <i>Alteromonas</i> Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs
Cited by: 16
Author(s): Ruijie Ma, Jiayong Lai, Xiaowei Chen, Long Wang, Yue Yang, Shuzhen Wei, Nianzhi Jiao, Rui Zhang
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pone.0199585

Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials
Cited by: 6
Author(s): John E. Holland, Qinxin Pan, Gevorg Grigoryan
Software Mentions: 3
Published: almost 6 years ago

10.1534/g3.119.400224

Contraction of the ROS Scavenging Enzyme Glutathione<i>S</i>-Transferase Gene Family in Cetaceans
Cited by: 11
Author(s): Ran Tian, Inge Seim, Wenhua Ren, Shixia Xu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2019.00293

Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis
Cited by: 17
Author(s): Marina Klemenčič, Johannes Asplund-Samuelsson, Marko Dolinar, Christiane Funk
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-58138-9

Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition
Cited by: 26
Author(s): Pooja Kesari, Shivendra Pratap, Poonam Dhankhar, Vikram Dalal, Manisha Mishra, Pradyumna Kumar Singh, Harsh Chauhan, Pravindra Kumar
Software Mentions: 3
Published: over 4 years ago

10.1016/j.cell.2020.10.004

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
Cited by: 394
Author(s): Abhik Banerjee, Mario R. Blanco, Emily A. Bruce, Drew D. Honson, Linlin M. Chen, Amy Chow, Prashant Bhat, Noah Ollikainen, Sofia A. Quinodoz, Colin Loney, Jasmine Thai, Zachary D. Miller, Aaron E. Lin, Madaline M Schmidt, Douglas G. Stewart, Daniel Goldfarb, Giuditta De Lorenzo, Suzannah J. Rihn, R.M. Voorhees, Jason Botten, Devdoot Majumdar, Mitchell Guttman
Software Mentions: 3
Published: over 3 years ago

10.1007/s00044-021-02715-8

n-Propyl 6-amino-2,6-dideoxy-2,2-difluoro-β-d-glucopyranoside is a good inhibitor for the β-galactosidase from E. coli
Cited by: 2
Author(s): Immo Serbian, Erik Prell, Cornelius Fischer, Hans‐Peter Deigner, René Csuk
Software Mentions: 3
Published: about 3 years ago

10.6026/97320630015784

Molecular docking based virtual screening of the breast cancer target NUDT5
Cited by: 6
Author(s): Razia Sultana, Monjia Islam, Md Azizul Haque, Fatematuz Zuhura Evamoni, Zahid Mohammad Imran, Jabunnesa Khanom, Adnan Munim
Software Mentions: 3
Published: over 4 years ago

10.1155/2020/2758640

A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification
Cited by: 6
Author(s): Shuyu Liu, Xiaohong Hu, Xiaotian Fan, Ruiqi Jin, Wenqian Yang, Yifei Geng, Jiarui Wu
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13072-016-0051-y

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
Cited by: 51
Author(s): Takashi Urahama, Akihito Harada, Kazuhira Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimurâ, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 3
Published: over 8 years ago

10.1155/2019/1205942

PIM1, CYP1B1, and HSPA2 Targeted by Quercetin Play Important Roles in Osteoarthritis Treatment by<i> Achyranthes bidentata</i>
Cited by: 7
Author(s): Dujun Ma, Yu Tian, Liping Peng, Lixin Wang, Zhouwei Liao, Wenming Xu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0023779

Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK
Cited by: 38
Author(s): Mónica Galiano, Paul‐Michael Agapow, Catherine Thompson, Steven G. Platt, Anthony Underwood, Joanna Ellis, Richard Myers, Jonathan Green, Maria Zambon
Software Mentions: 3
Published: over 12 years ago

10.1107/S205225251700570X

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation
Cited by: 123
Author(s): José M. Martín-García, Chelsie E. Conrad, Garrett Nelson, Natasha Stander, Nadia A. Zatsepin, James Zook, Liya Zhu, James H. Geiger, Eugene Chun, David J. Kissick, Mark Hilgart, Craig M. Ogata, Andrii Ishchenko, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse Coe, Ganesh Subramanian, Alexander F. Schäffer, Daniel James, Gihan Ketwala, Nagarajan Venugopalan, Shenglan Xu, Stephen Corcoran, D.R. Ferguson, Uwe Weierstall, John C. H. Spence, Vadim Cherezov, Petra Fromme, Robert F. Fischetti, Wei Liu
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0102856

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective
Cited by: 23
Author(s): Ashutosh Srivastava, Somdatta Sinha
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0080947

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity
Cited by: 43
Author(s): T. Vognsen, Ingvar R. Möller, Ole Kristensen
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms20225734

A Single Synonymous Variant (c.354G&gt;A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms19113340

Physical Background of the Disordered Nature of “Mutual Synergetic Folding” Proteins
Cited by: 6
Author(s): Csaba Magyar, Anikó Mentes, Erzsébet Fichó, Miklós Cserző, István Simon
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms20081996

Two Sides of the Coin: Ezrin/Radixin/Moesin and Merlin Control Membrane Structure and Contact Inhibition
Cited by: 45
Author(s): Katharine A. Michie, Adam Bermeister, Neil O. Robertson, Sophia C. Goodchild, Paul M. G. Curmi
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0243085

Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions
Cited by: 7
Author(s): Jin-Hyun Kim, Joo-Seok Park, Chang Kyu Lee, Min‐Gyun Jeong, Jiu Liang Xu, Yong-Soo Choi, Han‐Sung Jung, Hyunju Choi
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0022201

A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase
Cited by: 50
Author(s): Jesse D. Bloom, Jagannath S. Nayak, David Baltimore
Software Mentions: 3
Published: almost 13 years ago

10.1002/humu.24140

New variants and in silico analyses in GRK1 associated Oguchi disease
Cited by: 7
Author(s): James A. Poulter, Molly S. C. Gravett, Rachel L. Taylor, Kaoru Fujinami, Julie De Zaeytijd, James Bellingham, Atta Ur Rehman, Takaaki Hayashi, Mineo Kondo, Abdur Rehman, Muhammad Ansar, Dan Donnelly, Carmel Toomes, Manir Ali, Elfride De Baere, Bart P. Leroy, Nigel Davies, Robert Henderson, Andrew R. Webster, Carlo Rivolta, Omar Abdul Rahman Mahroo, Gavin Arno, Graeme C M Black, Martin McKibbin, Sarah A. Harris, Kamron Khan, Chris F. Inglehearn
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-64034-z

Comparative Analyses of the Conformational Dynamics Between the Soluble and Membrane-Bound Cytokine Receptors
Cited by: 7
Author(s): Chao‐Yie Yang
Software Mentions: 3
Published: about 4 years ago

10.1107/S2052252519007668

Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder
Cited by: 10
Author(s): Jeong Kuk Park, Keon Young Kim, Yeo Won Sim, Young Dong Kim, Jin Kyun Kim, Cheol Lee, Jeongran Han, Chae Un Kim, J. Eugene Lee, SangYoun Park
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-48155-8

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
Cited by: 11
Author(s): Carsten Krichel, Christina Möckel, Oliver Schillinger, Pitter F. Huesgen, Heinrich Sticht, Birgit Strodel, Oliver H. Weiergräber, Dieter Willbold, Philipp Neudecker
Software Mentions: 3
Published: over 4 years ago

10.1126/sciadv.aav8421

HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C
Cited by: 44
Author(s): M Collier, T. Reid Alderson, Carin Pamela de Villiers, D Nicholls, Heidi Y. Gastall, Timothy M. Allison, Matteo T. Degiacomi, Jiang He, Georg Mlynek, Dieter O. Fürst, Peter F.M. van der Ven, Kristina Djinović-Carugo, Andrew J. Baldwin, Hugh Watkins, Katja Gehmlich, Justin L. P. Benesch
Software Mentions: 3
Published: about 5 years ago

10.1038/srep13652

Dimeric interactions and complex formation using direct coevolutionary couplings
Cited by: 72
Author(s): Ricardo Nascimento dos Santos, Faruck Morcos, Biman Jana, Adriano D. Andricopulo, José N. Onuchic
Software Mentions: 3
Published: over 8 years ago

10.1107/S2052252521005297

Fixed-target serial femtosecond crystallography using <i>in cellulo</i> grown microcrystals
Cited by: 7
Author(s): Janine Mia Lahey-Rudolph, Robert Schönherr, Miriam Barthelmeß, P. Fischer, Carolin Seuring, Armin Wagner, A. Meents, Lars Redecke
Software Mentions: 3
Published: almost 3 years ago

10.1093/jxb/ery353

Homology modeling and<i>in vivo</i>functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase
Cited by: 20
Author(s): Gilles Lekeux, Jean-Marc Crowet, Cécile Nouet, Marine Joris, Alice Jadoul, Bernard Bosman, Monique Carnol, Patrick Motté, Laurence Lins, Moreno Galleni, Marc Hanikenne
Software Mentions: 3
Published: over 5 years ago

10.1093/ve/vev006

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
Cited by: 29
Author(s): Austin G. Meyer, Scott R. Spielman, Trevor Bedford, Claus O. Wilke
Software Mentions: 3
Published: over 9 years ago

10.1007/s10822-016-9900-9

1001 Ways to run AutoDock Vina for virtual screening
Cited by: 122
Author(s): Mohammad Mahdi Jaghoori, Boris Bleijlevens, Sílvia D. Olabarriaga
Software Mentions: 3
Published: about 8 years ago

10.1186/s13321-019-0354-7

Bayesian optimization for conformer generation
Cited by: 34
Author(s): Lucian Chan, Geoffrey Hutchison, Garrett M. Morris
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes12010034

Biological Regulatory Network (BRN) Analysis and Molecular Docking Simulations to Probe the Modulation of IP3R Mediated Ca2+ Signaling in Cancer
Cited by: 2
Author(s): Humaira Ismatullah, Ishrat Jabeen, Muhammad Saeed
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2019.00466

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling
Cited by: 34
Author(s): Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0032858

Molecular and Antigenic Characterization of Reassortant H3N2 Viruses from Turkeys with a Unique Constellation of Pandemic H1N1 Internal Genes
Cited by: 17
Author(s): Yohannes Berhane, Helen Kehler, Katherine Handel, Tamiko Hisanaga, Wanhong Xu, Davor Ojkić, John Pasick
Software Mentions: 3
Published: about 12 years ago

10.3390/ijms21082764

Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function
Cited by: 11
Author(s): Taremekedzwa Allan Sanyanga, Özlem Tastan Bishop
Software Mentions: 3
Published: about 4 years ago

10.3389/fmolb.2020.603983

Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors
Cited by: 1
Author(s): Mariem Ghoula, Axelle Le Marec, Christophe Magnan, Hervé Le Stunff, Olivier Taboureau
Software Mentions: 3
Published: over 3 years ago

10.3389/fmolb.2021.711975

Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels
Cited by: 6
Author(s): Michael Bründl, Sarala Pellikan, Anna Stary-Weinzinger
Software Mentions: 3
Published: almost 3 years ago

10.1107/S205225251900246X

Subatomic resolution X-ray structures of green fluorescent protein
Cited by: 24
Author(s): Kiyotsugu Takaba, Yang Tai, Haruhiko Eki, Hoang Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2016.00266

Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat
Cited by: 14
Author(s): Mariateresa Volpicella, Immacolata Fanizza, Claudia Leoni, Ágata Gadaleta, Domenica Nigro, B. Gattulli, Giacomo Mangini, Antonio Blanco, Luigi R. Ceci
Software Mentions: 3
Published: about 8 years ago

10.1111/mpp.12868

Comparative transcriptome profiling uncovers a <i>Lilium regale</i> NAC transcription factor, <i>LrNAC35</i>, contributing to defence response against cucumber mosaic virus and tobacco mosaic virus
Cited by: 25
Author(s): Daoyang Sun, Xinguo Zhang, Qingyu Zhang, Xiaotong Ji, Yuping Jia, Hong Wang, Lixin Niu, Yanlong Zhang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-60768-y

Complex approach for analysis of snake venom α-neurotoxins binding to HAP, the high-affinity peptide
Cited by: 9
Author(s): Denis S. Kudryavtsev, Valentin М. Tabakmakher, Gleb S. Budylin, N. S. Egorova, Roman G. Efremov, Igor A. Ivanov, Svetlana Yu. Belukhina, Artjom V. Jegorov, Igor E. Kasheverov, Elena V. Kryukova, Irina V. Shelukhina, Evgeny A. Shirshin, Nadezhda G. Zhdanova, Maxim N. Zhmak, Victor I. Tsetlin
Software Mentions: 3
Published: about 4 years ago

10.1083/jcb.202005130

SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase
Cited by: 4
Author(s): Shaowu Xue, Menglu Wang, Claudia Schaffner, Olga O. Nerusheva, Dean Clift, Christos Spanos, David A. Kelly, Michael H. Tatham, Andreas U. Wallek, Yehui Wu, Juri Rappsilber, A. Arockia Jeyaprakash, Zuzana Storchová, Ronald T. Hay, Adèle L. Marston
Software Mentions: 3
Published: about 3 years ago

10.1126/sciadv.aaq0762

Structures of monomeric and oligomeric forms of the <i>Toxoplasma gondii</i> perforin-like protein 1
Cited by: 28
Author(s): Ni Tien, Sophie I. Williams, Saša Rezelj, Gregor Anderluh, K. Harlos, Phillip J. Stansfeld, Robert J.C. Gilbert
Software Mentions: 3
Published: about 6 years ago

10.1186/s13321-016-0157-z

Ligand-based virtual screening interface between PyMOL and LiSiCA
Cited by: 9
Author(s): Athira Athira, Samo Lešnik, Tanja Štular, Dušanka Janežič, Janez Konc
Software Mentions: 3
Published: over 7 years ago

10.3390/md18070349

Interactions of the α3β2 Nicotinic Acetylcholine Receptor Interfaces with α-Conotoxin LsIA and its Carboxylated C-terminus Analogue: Molecular Dynamics Simulations
Cited by: 3
Author(s): Jierong Wen, David J. Adams, Andrew Hung
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: almost 5 years ago

10.1007/s10822-018-0148-4

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Cited by: 19
Author(s): Panagiotis I. Koukos, Xue Li, Alexandre M. J. J. Bonvin
Software Mentions: 3
Published: over 5 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase <i>Ce</i>Cht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: over 3 years ago

10.1093/jxb/eru266

Experimental and bioinformatic characterization of a recombinant polygalacturonase-inhibitor protein from pearl millet and its interaction with fungal polygalacturonases
Cited by: 8
Author(s): S. Prabhu, Ratna Singh, Stephan Kolkenbrock, Neerakkal Sujeeth, Nour Eddine El Gueddari, Bruno M. Moerschbacher, K. Ramachandra Kini, Martin Wagenknecht
Software Mentions: 3
Published: almost 10 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: about 7 years ago

10.1016/j.jmb.2016.12.004

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures
Cited by: 307
Author(s): Harry Jubb, Alícia P. Higueruelo, Bernardo Ochoa‐Montaño, William R. Pitt, David B. Ascher, Tom L. Blundell
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.22964

Dilation of fusion pores by crowding of SNARE proteins
Cited by: 54
Author(s): Zhenyong Wu, Oscar Bello, Sathish Thiyagarajan, Sarah M. Auclair, Wensi Vennekate, Shyam S. Krishnakumar, Ben O’Shaughnessy, Erdem Karatekin
Software Mentions: 3
Published: about 7 years ago

10.1107/S205225252000072X

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Cited by: 31
Author(s): Alexander M. Wolff, I.D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, J.T. Biel, Sergio Carbajo, Aina E. Cohen, S.V. Cortez, Ana González, Tsuneo Hino, Dohyun Im, Jake Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, R. Tanaka, Erin Thompson, H. van den Bedem, R.A. Woldeyes, Fumiaki Yumoto, Zhao Wei, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.02858-18

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
Cited by: 13
Author(s): Pierrick Craveur, A.T. Gres, Karen A. Kirby, Dandan Liu, John A. Hammond, Yisong Deng, Stefano Forli, David S. Goodsell, James R. Williamson, Stefan G. Sarafianos, Arthur J. Olson
Software Mentions: 3
Published: about 5 years ago