10.1155/2014/402492

Prediction of Epitope-Based Peptides for the Utility of Vaccine Development from Fusion and Glycoprotein of Nipah Virus Using<i>In Silico</i>Approach
Cited by: 38
Author(s): M. Sadman Sakib, Md. Rezaul Islam, A. K. M. Mahbub Hasan, A.H.M. Nurun Nabi
Software Mentions: 3
Published: about 12 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

10.1186/1472-6807-5-19

Natural history of S-adenosylmethionine-binding proteins
Cited by: 240
Author(s): Piotr Koźbiał, Arcady Mushegian
Software Mentions: 3
Published: almost 21 years ago

10.1186/s13068-017-0944-4

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity
Cited by: 29
Author(s): Bruno Luan Mello, Anna Alessi, Diego Mauricio Riaño‐Pachón, Eduardo R. deAzevedo, Francisco Eduardo Gontijo Guimarães, Melissa C. Espirito Santo, Simon J. McQueen‐Mason, Neil C. Bruce, Igor Polikarpov
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0229467

Discovery of antitumor lectins from rainforest tree root transcriptomes
Cited by: 3
Author(s): Atip Lawanprasert, Caitlin A. Guinan, Erica A. Langford, Carly E. Hawkins, Janna N. Sloand, Howard W. Fescemyer, Matthew R. Aronson, Jacob A. Halle, James H. Marden, Scott H. Medina
Software Mentions: 3
Published: over 6 years ago

10.1107/S2059798318006678

Engineering glycoside hydrolase stability by the introduction of zinc binding
Cited by: 1
Author(s): Thomas L. Ellinghaus, J.H. Pereira, R.P. McAndrew, Ditte Hededam Welner, Andy DeGiovanni, Joel M. Guenther, Huu M. Tran, Taya Feldman, Blake A. Simmons, Kenneth L. Sale, Paul D. Adams
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0039550

On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase
Cited by: 74
Author(s): Patrick Schaub, Qiuju Yu, Sandra Gemmecker, Pierre Poussin-Courmontagne, J. Mailliot, A.G. McEwen, Sandro Ghisla, Salim Al‐Babili, Jean Cavarelli, Peter Beyer
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0232959

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability
Cited by: 7
Author(s): Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
Software Mentions: 3
Published: over 6 years ago

10.1186/1754-6834-7-18

Close relationship of a novel Flavobacteriaceaeα-amylase with archaeal α-amylases and good potentials for industrial applications
Cited by: 28
Author(s): Chunfang Li, Miaofen Du, Bin Cheng, Lushan Wang, Xinqiang Liu, Cuiqing Ma, Chunyu Yang, Ping Xu
Software Mentions: 3
Published: over 12 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: about 8 years ago

10.1186/s12859-019-3120-y

RNA 3D structure prediction guided by independent folding of homologous sequences
Cited by: 18
Author(s): Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
Software Mentions: 3
Published: almost 7 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 9 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: over 9 years ago

10.1093/aobpla/plz075

Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava
Cited by: 8
Author(s): Ming-You Dong, Xian‐Wei Fan, Xiang-Yu Pang, Youzhi Li
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1008476

Past and ongoing adaptation of human cytomegalovirus to its host
Cited by: 18
Author(s): Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell’Oste, Chiara Pontremoli, Chiara Vantaggiato, Diego Forni, Mario Clerici, Santo Landolfo, Manuela Sironi
Software Mentions: 3
Published: over 6 years ago

10.1107/S0907444911056058

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in<i>BUSTER</i>
Cited by: 529
Author(s): Oliver S. Smart, Thomas Womack, Claus Flensburg, Peter M. Keller, W. A. Paciorek, A. Sharff, Clemens Vonrhein, G. Bricogne
Software Mentions: 3
Published: over 14 years ago

10.1107/S1744309113012931

Structure of PatF from<i>Prochloron didemni</i>
Cited by: 26
Author(s): Andrew F. Bent, Jesko Koehnke, Wael E. Houssen, Margaret Caroline MacHin Smith, Marcel Jaspars, James H. Naismith
Software Mentions: 3
Published: about 13 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

10.1042/BSR20140088

Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen <i>Staphylococcus pseudintermedius</i>
Cited by: 29
Author(s): Francesca Abate, E. Malito, Roberta Cozzi, Paola Lo Surdo, Domenico Maione, Matthew J. Bottomley
Software Mentions: 3
Published: over 11 years ago

10.1016/j.bpj.2018.03.040

Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering
Cited by: 3
Author(s): Emma J. Sutton, Richard T. Bradshaw, Christian M. Orr, Björn Frendéus, Gunilla Larsson, Ingrid Teige, Mark S. Cragg, Ivo Tews, Jonathan W. Essex
Software Mentions: 3
Published: about 8 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: about 7 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: about 10 years ago

10.1371/journal.ppat.1009723

ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Cited by: 17
Author(s): Daniel J. Rawle, Thuy T. Le, Troy Dumenil, Kexin Yan, Bing Tang, Wilson Nguyen, Daniel Watterson, Naphak Modhiran, Jody Hobson‐Peters, Cameron Bishop, Andreas Suhrbier
Software Mentions: 3
Published: about 5 years ago

10.1107/S1399004714016241

Conformation-independent structural comparison of macromolecules with<i>ProSMART</i>
Cited by: 150
Author(s): Robert A. Nicholls, Marcus Fischer, Stuart McNicholas, Garib N. Murshudov
Software Mentions: 3
Published: almost 12 years ago

10.1107/S2053230X20001466

Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization
Cited by: 4
Author(s): A.N. Mitropoulou, Tom Ceska, James T. Heads, Andrew J. Beavil, Alistair J. Henry, James M. McDonnell, Brian J. Sutton, Anna M. Davies
Software Mentions: 3
Published: over 6 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: almost 7 years ago

10.1186/s12859-016-0898-8

Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Cited by: 22
Author(s): Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf‐Dieter Schubert, Alan Christoffels
Software Mentions: 3
Published: over 10 years ago

10.1016/j.bpj.2018.09.002

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR
Cited by: 3
Author(s): Graham M. Saunders, Hannah E. Bruce Macdonald, Jonathan W. Essex, Syma Khalid
Software Mentions: 3
Published: almost 8 years ago

10.3390/biom11070929

Discovery of Novel Allosteric Modulators Targeting an Extra-Helical Binding Site of GLP-1R Using Structure- and Ligand-Based Virtual Screening
Cited by: 7
Author(s): Qingtong Zhou, Wei Guo, Antao Dai, Xiaoqing Cai, Márton Vass, Chris de Graaf, Shui Wang, Suwen Zhao, Dehua Yang, Ming Wei Wang
Software Mentions: 3
Published: 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 6 years ago

10.1107/S0907444910000302

Rapid model building of β-sheets in electron-density maps
Cited by: 4
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 years ago

10.1016/j.jmb.2015.08.023

Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain
Cited by: 9
Author(s): Nora Cronin, Jing Yang, Ziguo Zhang, Kiran Kulkarni, Leifu Chang, Hiroyuki Yamano, David Barford
Software Mentions: 3
Published: almost 11 years ago

10.1128/mBio.00373-17

Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus
Cited by: 243
Author(s): Simon J. Anthony, Kirsten Gilardi, Vineet D. Menachery, Tracey Goldstein, Benard Ssebide, R. Mbabazi, Isamara Navarrete-Macias, Eliza Liang, Heather L. Wells, Alan C. Hicks, Alexandra Petrosov, Denis K. Byarugaba, Kari Debbink, Kenneth H. Dinnon, Trevor Scobey, Scott H. Randell, Boyd Yount, Michael R. Cranfield, Christine K. Johnson, Ralph S. Baric, W. Ian Lipkin, Jonna A. K. Mazet
Software Mentions: 3
Published: over 9 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 13 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

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12915-021-01102-4

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
Cited by: 9
Author(s): Hüseyin İlgü, Jean-Marc Jeckelmann, David Kalbermatter, Zöhre Ucurum, Thomas Lemmin, Dimitrios Fotiadis
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms21176185

Characterization of Two Novel Variants of the Steroidogenic Acute Regulatory Protein Identified in a Girl with Classic Lipoid Congenital Adrenal Hyperplasia
Cited by: 3
Author(s): Efstathios Katharopoulos, Natascia Di Iorgi, Paula Fernández-Álvarez, Amit V. Pandey, Michael Groessl, Shraddha Dubey, Núria Camats, Flavia Napoli, Giuseppa Patti, Marilea Lezzi, Mohamad Maghnie, Christa E. Flück
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21207683

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450
Cited by: 12
Author(s): Sergey Bukhdruker, Tatsiana Varaksa, Irina Grabovec, Egor Marin, Polina Shabunya, Maria Kadukova, Sergei Grudinin, Anton Kavaleuski, Anastasiia Gusach, Andrei A. Gilep, Valentin Borshchevskiy, Natallia Strushkevich
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22083812

Crystal Structure of the Epo1-Bem3 Complex for Bud Growth
Cited by: 0
Author(s): Jin Wang, Lei Li, Zhenhua Ming, Lijie Wu, Liming Yan
Software Mentions: 3
Published: over 5 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 6 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: about 5 years ago

10.1002/jmr.2696

The evolutionary characteristics and structural biology of <i>Gallus</i> toll-like receptor 21
Cited by: 6
Author(s): Hongping Wu, Hai Wang, Weibo Jiang, Zhengxing Lian
Software Mentions: 3
Published: over 8 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: over 9 years ago

10.1128/mBio.03066-19

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Cited by: 45
Author(s): José A. Gavira, Vadim M. Gumerov, Míriam Rico-Jiménez, Marharyta Petukh, Amit A. Upadhyay, Álvaro Ortega, Miguel A. Matilla, Igor B. Zhulin, Tino Krell
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.58362

Structural basis of mitochondrial translation
Cited by: 61
Author(s): Shintaro Aibara, Vivek P. Singh, A. Modelska, Alexey Amunts
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms21124378

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone
Cited by: 19
Author(s): Yen-Chi Tsao, Yu‐Jung Chang, Chun-Hsien Wang, Linyi Chen
Software Mentions: 3
Published: about 6 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: over 9 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: over 6 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: almost 7 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: about 6 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

10.1371/journal.ppat.1009775

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
Cited by: 10
Author(s): Sofia Banchenko, Ferdinand Krupp, Christine Gotthold, Jörg Bürger, Andrea Graziadei, Francis J. O’Reilly, Ludwig Sinn, Olga Ruda, Juri Rappsilber, C.M.T. Spahn, Thorsten Mielke, Ian A. Taylor, David Schwefel
Software Mentions: 3
Published: about 5 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: about 7 years ago

10.1016/j.str.2021.04.004

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein
Cited by: 8
Author(s): Patryk Ludzia, E.D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Software Mentions: 3
Published: almost 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 5 years ago

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with <i>phenix.refine</i>
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 14 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: about 12 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

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: almost 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

10.1155/2014/697532

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: over 12 years ago

10.1093/gbe/evv046

OASes and STING: Adaptive Evolution in Concert
Cited by: 38
Author(s): Alessandra Mozzi, Chiara Pontremoli, Diego Forni, Mario Clerici, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: over 11 years ago

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 5 years ago

10.1093/gbe/evaa038

The Evolution History of Fe–S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs
Cited by: 3
Author(s): Hui‐Meng Lu, Jing-Di Li, Yu-Dan Zhang, Xiaoli Lü, Chang Xu, Yuan Huang, Michael Gribskov
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.620472

Case Report: Novel RPGRIP1L Gene Mutations Identified by Whole Exome Sequencing in a Patient With Multiple Primary Tumors
Cited by: 0
Author(s): Jianghong Guo, Yu Ye, Zhuqing Ji, Ming Yao, Xiaotian Xia, Xiaofeng Sha, Ming‐De Huang
Software Mentions: 3
Published: over 5 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: about 7 years ago

10.3389/fgene.2020.568052

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia
Cited by: 7
Author(s): Xinmiao Fan, Ping Lu, Hao Sun, Yu‐Shan Chen, Pu Wang, Tao Liu, Rui Jiang, Xuegong Zhang, Xiaowei Chen
Software Mentions: 3
Published: almost 6 years ago

10.1093/gbe/evaa095

Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains
Cited by: 3
Author(s): Cameron J. Weadick
Software Mentions: 3
Published: over 6 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: almost 6 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 5 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 10 years ago

10.3390/ijms22062861

In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus
Cited by: 5
Author(s): Colleen Varaidzo Manyumwa, Özlem Tastan Bishop
Software Mentions: 3
Published: over 5 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/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

10.1016/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

10.1371/journal.pone.0116688

Identification of STAT1 and STAT3 Specific Inhibitors Using Comparative Virtual Screening and Docking Validation
Cited by: 29
Author(s): Małgorzata Szeląg, Anna Czerwoniec, Joanna Wesoły, Hans A.R. Bluyssen
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: over 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: over 11 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: about 5 years ago

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 11 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 9 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: about 5 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: about 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

10.3389/fchem.2020.597495

Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations
Cited by: 4
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-9-352

Alignment of protein structures in the presence of domain motions
Cited by: 48
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Software Mentions: 3
Published: almost 18 years ago

10.1107/S1399004715005210

<i>In meso in situ</i> serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 11 years ago

10.3389/fphar.2017.00393

Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket
Cited by: 6
Author(s): Tamir Dingjan, Anne Imberty, Serge Pérez, Elizabeth Yuriev, Paul A. Ramsland
Software Mentions: 3
Published: about 9 years ago

10.1186/1472-6807-11-33

Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria
Cited by: 5
Author(s): Yu Song, A. Vit, Sean R. A. Devenish, H. K. Mahanty, Aymelt Itzen, Roger S. Goody, Wulf Blankenfeldt
Software Mentions: 3
Published: about 15 years ago

10.1093/gbe/evu235

Albuminoid Genes: Evolving at the Interface of Dispensability and Selection
Cited by: 12
Author(s): Alessandra Mozzi, Diego Forni, Rachele Cagliani, Jacopo Vertemara, Nereo Bresolin, Manuela Sironi
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13040-020-00227-6

Examining the effector mechanisms of Xuebijing injection on COVID-19 based on network pharmacology
Cited by: 30
Author(s): Wenjiang Zheng, Qian Yan, Yongshi Ni, Shaofeng Zhan, Liuliu Yang, Hongfa Zhuang, Xiaohong Liu, Yong Jiang
Software Mentions: 3
Published: almost 6 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

10.1107/S0907444910000272

Rapid chain tracing of polypeptide backbones in electron-density maps
Cited by: 5
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 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: over 5 years ago

10.1371/journal.ppat.1009566

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses
Cited by: 4
Author(s): Johanna West, Juliane Röder, Tatyana Matrosovich, Jana Beicht, Jan Baumann, Nancy Mounogou Kouassi, Jennifer Doedt, Nicolai V. Bovin, Gianpiero Zamperin, Michele Gastaldelli, Annalisa Salviato, Francesco Bonfante, Sergei L. Kosakovsky Pond, Sander Herfst, Ron A. M. Fouchier, Jochen Wilhelm, Hans‐Dieter Klenk, Mikhail Matrosovich
Software Mentions: 3
Published: almost 5 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