10.1186/s13073-014-0081-7

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach
Cited by: 31
Author(s): Huy Gia Vuong, Feixiong Cheng, Lin Chen, Zhongming Zhao
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13062-020-00267-2

AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4
Cited by: 87
Author(s): Mario S. Valdés-Tresanco, Mario E. Valdés‐Tresanco, Pedro A. Valiente, Ernesto Moreno
Software Mentions: 4
Published: about 6 years ago

10.1093/bioinformatics/bty347

Applying graph theory to protein structures: an Atlas of coiled coils
Cited by: 15
Author(s): Jack W. Heal, Gail J. Bartlett, Christopher W. Wood, Andrew Thomson, Derek N. Woolfson
Software Mentions: 4
Published: over 8 years ago

10.12688/f1000research.12301.2

In silico analysis of natural compounds targeting structural and nonstructural proteins of chikungunya virus
Cited by: 16
Author(s): Jaspreet Jain, Anchala Kumari, Pallavi Somvanshi, Abhinav Grover, S. Somnath Pai, Sujatha Sunil
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcimb.2021.605589

Disseminated Talaromyces marneffei Infection in a Non-HIV Infant With a Homozygous Private Variant of RELB
Cited by: 9
Author(s): Xiaojuan Ding, Han Huang, Lili Zhao, Min Chen, Fang Peng, Bing Zhang, Xinyu Cui, Xiu‐An Yang
Software Mentions: 3
Published: over 5 years ago

10.1016/j.febslet.2015.11.030

Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli
Cited by: 13
Author(s): Cristina Ortiz, Danguole Kureisaite-Ciziene, Florian Schmitz, Stephen H. McLaughlin, Miguel Vicente, Jan Löwe
Software Mentions: 3
Published: almost 11 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: almost 8 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: almost 6 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: almost 8 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: 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: over 5 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: almost 6 years ago

10.1111/febs.15514

Structure‐based design of peptides that trigger <i>Streptococcus pneumoniae</i> cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 6 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: almost 10 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: over 11 years ago

10.1371/journal.pone.0217164

Three genetically distinct ferlaviruses have varying effects on infected corn snakes (Pantherophis guttatus)
Cited by: 7
Author(s): Michael Pees, Volker Schmidt, Tibor Papp, Ákos Gellért, Maha Diekan Abbas, J. Matthias Starck, Annkatrin Neul, Rachel E. Marschang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0165020

Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants
Cited by: 32
Author(s): Hongwu Du, Feng Ran, Hongli Dong, Jing Wen, Jiana Li, Zhe Liang
Software Mentions: 3
Published: almost 10 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: almost 9 years ago

10.1371/journal.pone.0043245

A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Cited by: 62
Author(s): Nemin Celik, Chaille T Webb, Denisse L. Leyton, Kathryn E. Holt, Eva Heinz, Rebecca J. Gorrell, Terry Kwok, Thomas Naderer, Richard A. Strugnell, Terence P. Speed, Rohan D. Teasdale, Vladimir A Likić, Trevor Lithgow
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0150634

Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants
Cited by: 4
Author(s): Preeti Arya, Vishal Acharya
Software Mentions: 3
Published: over 10 years ago

10.1093/gbe/evab125

Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System
Cited by: 9
Author(s): Carlos Santana-Molina, Fernando Gutiérrez, Damien P. Devos
Software Mentions: 3
Published: over 5 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: over 7 years ago

10.1371/journal.pone.0097817

Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning
Cited by: 12
Author(s): HyeonSeok Shin, Yoobok Cho, Donghui Choe, Yu‐Jin Jeong, Suhyung Cho, Sun Chang Kim, Byung-Kwan Cho
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 12 years ago

10.3390/molecules23112954

Molecular Modeling and In Vitro Studies of a Neutral Oxime as a Potential Reactivator for Acetylcholinesterase Inhibited by Paraoxon
Cited by: 15
Author(s): Reuel L. de Paula, Joyce S. F. D. de Almeida, Samir F. A. Cavalcante, Arlan da Silva Gonçalves, Alessandro B. C. Simas, Tanos C. C. França, Martin Vališ, Kamil Kuča, Eugenie Nepovimová, José Mauro Granjeiro
Software Mentions: 3
Published: almost 8 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 5 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: over 5 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: over 12 years ago

10.1038/s41598-018-29058-6

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-08842-w

Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach
Cited by: 226
Author(s): Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Software Mentions: 3
Published: about 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: over 10 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: over 6 years ago

10.1371/journal.pcbi.1004805

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cited by: 73
Author(s): Vaclav Cvicek, William A. Goddard, Ravinder Abrol
Software Mentions: 3
Published: over 10 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: over 7 years ago

10.3390/ijms22168631

The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: about 5 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 9 years ago

10.1371/journal.pone.0172743

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Cited by: 35
Author(s): Akshay Sridhar, Gregory A. Ross, Philip C. Biggin
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0140934

Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice
Cited by: 40
Author(s): Yue Chen, Xiaoman Wang, Li Zhou, Yi He, Dun Wang, Yanhua Qi, Dongxiang Jiang
Software Mentions: 3
Published: almost 11 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: over 6 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: almost 8 years ago

10.3390/ijms22189833

Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Cited by: 0
Author(s): Joanna Drabinska, Kamil Steczkiewicz, Martyna Kujawa, Elżbieta Kraszewska
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0082341

Targeting a Cross-Reactive Gly m 5 Soy Peptide as Responsible for Hypersensitivity Reactions in a Milk Allergy Mouse Model
Cited by: 21
Author(s): Renata Curciarello, Paola Lorena Smaldini, Ángela María Candreva, Vicente Ferreira González, Gustavo Parisi, Ana Cauerhff, Ivana Analía Barrios, Luis Enrique Bruno Blanch, Carlos A. Fossati, Silvana Petruccelli, Guillermo Horacio Docena
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0035974

The Hepatitis E Virus Polyproline Region Is Involved in Viral Adaptation
Cited by: 74
Author(s): Michael A. Purdy, James Lara, Yury Khudyakov
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0236894

A chemical interpretation of protein electron density maps in the worldwide protein data bank
Cited by: 5
Author(s): Sen Yao, Hunter N. B. Moseley
Software Mentions: 3
Published: about 6 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: 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: about 5 years ago

10.1111/febs.13310

Inter‐domain electron transfer in cellobiose dehydrogenase: modulation by <scp>pH</scp> and divalent cations
Cited by: 49
Author(s): Daniel Kracher, Kawah Zahma, Christopher Schulz, Christoph Sygmund, Lo Gorton, Roland Ludwig
Software Mentions: 3
Published: over 11 years ago

10.1007/s00792-013-0542-8

The role of disulfide bond in hyperthermophilic endocellulase
Cited by: 13
Author(s): Han-Woo Kim, Kazuhiko Ishikawa
Software Mentions: 3
Published: over 13 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: over 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: over 6 years ago

10.1101/2021.02.21.432184

High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19
Cited by: 4
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0140359

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions
Cited by: 20
Author(s): Andrea Bazzoli, Simon Kelow, John Karanicolas
Software Mentions: 3
Published: almost 11 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: almost 14 years ago

10.1155/2014/697532

In SilicoAntitubercular Activity Analysis of Benzofuran and Naphthofuran Derivatives
Cited by: 5
Author(s): Prashantha Karunakar, C. R. Girija, Venkatappa Krishnamurthy, V. Krishna, K. V. Shivakumar
Software Mentions: 3
Published: almost 13 years ago

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-021-82125-3

Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides
Cited by: 9
Author(s): Anizah Rahumatullah, Dinesh Balachandra, Rahmah Noordin, Zamrina Baharudeen, Yee Ying Lim, Yee Siew Choong, Theam Soon Lim
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1009651

Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity
Cited by: 6
Author(s): Aaron D. Besterman, Thorsten Althoff, Peter Elfferich, Irma Gutierrez-Mejia, Joshua Sadik, Jonathan A. Bernstein, Yvette van Ierland, Anja A. Kattentidt-Mouravieva, Mark Nellist, Jeff Abramson, Julián A. Martínez-Agosto
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-46094-y

Human Corneal Expression of SLC4A11, a Gene Mutated in Endothelial Corneal Dystrophies
Cited by: 23
Author(s): Deepti Malhotra, Sampath K. Loganathan, Anthony M. Chiu, Chris M. Lukowski, Joseph R. Casey
Software Mentions: 3
Published: about 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: over 11 years ago

10.1038/s41598-020-68419-y

Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis
Cited by: 8
Author(s): Hye Lin Chun, So Yeon Lee, Sung Hoon Lee, Chang Sup Lee, Hyun Ho Park
Software Mentions: 3
Published: about 6 years ago

10.1016/j.str.2020.04.010

CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions
Cited by: 16
Author(s): Takashi Ochi, Valentina Quarantotti, Huawen Lin, Jérôme Jullien, Ivan Rosa e Silva, Francesco Boselli, Deepak D. Barnabas, Christopher M. Johnson, Stephen H. McLaughlin, Stefan Freund, Andrew N. Blackford, Yuu Kimata, Raymond E. Goldstein, Stephen Jackson, Tom L. Blundell, Susan K. Dutcher, Fanni Gergely, M. van Breugel
Software Mentions: 3
Published: over 6 years ago

10.1155/2014/162150

Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases
Cited by: 10
Author(s): Jamal Shamsara
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-019-39984-8

Insights into the dynamic nature of the dsRNA-bound TLR3 complex
Cited by: 27
Author(s): Vijayakumar Gosu, Seung‐Woo Son, Donghyun Shin, Ki Duk Song
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39588-2

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface
Cited by: 18
Author(s): Adam H. Barczewski, Michael J. Ragusa, Dale F. Mierke, Maria Pellegrini
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40432-w

Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-37506-6

Mechanism of action of the moonlighting protein EfTu as a Substance P sensor in Bacillus cereus
Cited by: 9
Author(s): Awa Ndiaye, Valérie Borrel, Pierre‐Jean Racine, Thomas Clamens, Ségolène Depayras, Olivier Maillot, Béatrice Schaack, Sylvie Chevalier, Olivier Lesouhaitier, Marc Feuilloley
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1006722

Identifying individual risk rare variants using protein structure guided local tests (POINT)
Cited by: 8
Author(s): Rachel West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger‐Reif, Denis Fourches, Jung Ying Tzeng
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-37699-w

The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
Cited by: 15
Author(s): Tyler Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40564-z

Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States
Cited by: 38
Author(s): Fangzhou Chen, Todd P. Knutson, Stephanie Rossow, Linda J. Saif, Douglas Marthaler
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-34508-2

“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Cited by: 16
Author(s): Yasaman Karami, Tristan Bitard‐Feildel, Élodie Laine, Alessandra Carbone
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-08747-8

Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters
Cited by: 56
Author(s): Venkata Krishnan Ramaswamy, Attilio Vittorio Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-29865-x

EPO does not promote interaction between the erythropoietin and beta-common receptors
Cited by: 18
Author(s): Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin R. Gillinder, Melissa Ilsley, Hayley S. Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhagat
Software Mentions: 3
Published: about 8 years ago

10.1038/srep38564

Structure and dynamics of a constitutively active neurotensin receptor
Cited by: 55
Author(s): Brian E. Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F. White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Software Mentions: 3
Published: almost 10 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: almost 6 years ago

10.1038/s41598-017-01640-4

Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
Cited by: 7
Author(s): L. Xue, Qingping Wu, Ruimin Dong, Weiping Cai, Haoming Wu, Moutong Chen, Gang Chen, Juan Wang, Jumei Zhang
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-36267-6

The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Cited by: 7
Author(s): Simranjit Singh, Simon Lämmle, Heiko Giese, Susanne Kämmerer, Stefanie Meyer-Roxlau, Ezzaldin Ahmed Alfar, Hassan Dihazi, Kaomei Guan, Ali El‐Armouche, Florian Richter
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1005294

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 3
Published: almost 10 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 6 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: over 7 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: about 10 years ago

10.1371/journal.pcbi.1004068

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
Cited by: 34
Author(s): Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming‐Sound Tsao, Igor Jurišica
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1004981

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
Cited by: 28
Author(s): Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati
Software Mentions: 3
Published: over 10 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: almost 8 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: almost 12 years ago

10.1038/s41598-018-29664-4

Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody
Cited by: 20
Author(s): Jiun-Bo Chen, Faruk Ramadani, M.O.Y. Pang, Rebecca L. Beavil, Mary D. Holdom, A.N. Mitropoulou, Andrew J. Beavil, Hannah J. Gould, Tse Wen Chang, Brian J. Sutton, James M. McDonnell, Anna M. Davies
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-33068-9

Spider silk proteome provides insight into the structural characterization of Nephila clavipes flagelliform spidroin
Cited by: 26
Author(s): José Roberto Aparecido dos Santos-Pinto, Helen Andrade Arcuri, Franciele Grego Esteves, Mário Sérgio Palma, Gert Lübec
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1007892

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
Cited by: 2
Author(s): Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008964

The evolution and functional divergence of the histone H2B family in plants
Cited by: 42
Author(s): Dazong Jiang, Michael Borg, Zdravko J. Lorković, Sean A. Montgomery, Akihisa Osakabe, Ramesh Yelagandula, Elin Axelsson, Frédéric Berger
Software Mentions: 3
Published: about 6 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: almost 7 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: over 11 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-39641-0

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1008140

A steady-state model of microbial acclimation to substrate limitation
Cited by: 13
Author(s): John R. Casey, Michael J. Follows
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1002708

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří­ Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: almost 14 years ago

10.1007/s13361-018-1910-5

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31
Cited by: 5
Author(s): Andrey Dyachenko, Sem Tamara, Albert J. R. Heck
Software Mentions: 3
Published: over 8 years ago

10.1172/jci.insight.97018

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site
Cited by: 16
Author(s): Hao Cheng, Sebastian K. Grimm, M.S.A. Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, G. Donofrio, Gunilla B. Karlsson Hedestam, Mattia Bonsignori, Barton F. Haynes, Timothy Lahey, Isaac Maro, C. Fordham von Reyn, Miroslaw K. Gorny, Susan Zolla‐Pazner, Bruce D. Walker, Galit Alter, Dennis R. Burton, Merlin L. Robb, Shelly J. Krebs, Michael S. Seaman, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 3
Published: over 8 years ago