pypi: Arpeggio | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000165

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection
Cited by: 45
Author(s): Jane Hawkey, David B. Ascher, Louise M. Judd, Ryan R. Wick, Xenia Kostoulias, Heather Cleland, Denis Spelman, Alex Padiglione, Anton Y. Peleg, Kathryn E. Holt
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.ppat.1009729

Definition of the immune evasion-replication interface of rabies virus P protein
Cited by: 10
Author(s): Jingyu Zhan, Angela R. Harrison, Stephanie Portelli, Thanh Bình Nguyễn, Isshu Kojima, Siqiong Zheng, Fei Yan, Tsutomu Matsui, Stephen M. Rawlinson, Ashish Sethi, Naoto Ito, David B. Ascher, Gregory W. Moseley, Paul R. Gooley
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-74648-y

Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches
Cited by: 20
Author(s): Stephanie Portelli, Yoochan Myung, Nicholas Furnham, Sundeep Chaitanya Vedithi, Douglas E V Pires, David B. Ascher
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-03575-6

Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures
Cited by: 5
Author(s): José Renato M. S. Barroso, Diego Mariano, Sandro Renato Dias, Rafael E. O. Rocha, Lucianna Helene Santos, R.A.P. Nagem, Raquel Cardoso de Melo‐Minardi
Software Mentions: 3
Published: over 4 years ago

10.1016/j.csbj.2020.11.013

HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae
Cited by: 13
Author(s): Sundeep Chaitanya Vedithi, Sony Malhotra, Marcin J. Skwark, Asma Munir, Marta Acebrón-García-de-Eulate, Vaishali P. Waman, Ali Alsulami, David B. Ascher, Tom L. Blundell
Software Mentions: 3
Published: almost 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: over 5 years ago

10.1016/j.str.2020.08.004

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics
Cited by: 14
Author(s): D E. Nicholson, Thomas A. Edwards, Alex J. O’Neill, Neil A. Ranson
Software Mentions: 3
Published: about 4 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: almost 8 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1009335

Ankyrin repeats in context with human population variation
Cited by: 4
Author(s): Javier S. Utgés, Maxim I. Tsenkov, Noah J. M. Dietrich, Stuart A. MacGowan, Geoffrey J. Barton
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0192488

The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity
Cited by: 7
Author(s): Igor Sabljić, Marko Tomin, Mihaela Matovina, Iva Sučec, Ana Tomašić Paić, Antonija Tomić, Marija Abramić, Sanja Tomić
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmolb.2021.643849

Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance
Cited by: 5
Author(s): Grace Mugumbate, Brilliant Nyathi, Albert Zindoga, Gadzikano Munyuki
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.ppat.1008086

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites
Cited by: 16
Author(s): Maryia Karpiyevich, Sophie H. Adjalley, Marco Mol, David B. Ascher, Bethany Mason, Gerbrand J. van der Heden van Noort, Heike Laman, Huib Ovaa, Marcus Lee, Katerina Artavanis‐Tsakonas
Software Mentions: 2
Published: about 5 years ago

10.1073/pnas.2101496118

Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation
Cited by: 29
Author(s): Linda Truebestein, Harald Hornegger, Dorothea Anrather, Markus Hartl, Kaelin D Fleming, Jordan T B Stariha, Els Pardon, Jan Steyaert, John E. Burke, Thomas A. Leonard
Software Mentions: 2
Published: over 3 years ago

10.1016/j.cell.2017.11.033

Pharmacogenomics of GPCR Drug Targets
Cited by: 411
Author(s): Alexander S. Hauser, Sreenivas Chavali, Ikuo Masuho, Leonie Johanna Jahn, Kirill A. Martemyanov, David E. Gloriam, M. Madan Babu
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-23423-1

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae
Cited by: 36
Author(s): Sundeep Chaitanya Vedithi, Sony Malhotra, Madhusmita Das, Sheela Daniel, Nanda B Kishore, Anuja George, Shantha Arumugam, Lakshmi Rajan, Mannam Ebenezer, David B. Ascher, Eddy Arnold, Tom L. Blundell
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-58635-x

Structure guided prediction of Pyrazinamide resistance mutations in pncA
Cited by: 46
Author(s): Malancha Karmakar, Carlos H M Rodrigues, Kristy Horan, Justin Denholm, David B. Ascher
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-89450-7

Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1
Cited by: 17
Author(s): Arunabh Choudhury, Taj Mohammad, Nikhil Samarth, Afzal Hussain, Tabish Rehman, Asimul Islam, Mohamed F. Alajmi, Shailza Singh, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: over 3 years ago

10.1038/s41396-020-00889-4

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Cited by: 60
Author(s): Heyu Lin, David B. Ascher, Yoochan Myung, Carl H. Lamborg, Steven J. Hallam, Caitlin M. Gionfriddo, Kathryn E. Holt, John W. Moreau
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.jmb.2019.10.005

Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins
Cited by: 4
Author(s): Laura J. Sherwood, Alexander B. Taylor, P. John Hart, Andrew Hayhurst
Software Mentions: 2
Published: almost 5 years ago

10.3390/molecules25204723

Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches
Cited by: 75
Author(s): Javier Vázquez, Michel Angel Lopez, Enric Gibert, Enric Herrero, F. Javier Luque
Software Mentions: 2
Published: about 4 years ago

10.3390/molecules23071690

Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study
Cited by: 22
Author(s): Alexander Eisold, Dirk Labudde
Software Mentions: 2
Published: over 6 years ago

10.3390/pharmaceutics13081182

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses
Cited by: 12
Author(s): Dhanik Reshamwala, Sailee Shroff, Olivier Sheik Amamuddy, Valentino Laquintana, Nunzio Denora, Antonella Zacheo, Vili Lampinen, Vesa P. Hytönen, Özlem Tastan Bishop, Silke Krol, Varpu Marjomäki
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22126312

Histamine: A Bacterial Signal Molecule
Cited by: 11
Author(s): Tino Krell, José A. Gavira, Félix Velando, Matilde Fernández, Amalia Roca, Elizabet Monteagudo‐Cascales, Miguel A. Matilla
Software Mentions: 1
Published: over 3 years ago

10.1042/BSR20190312

Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach
Cited by: 16
Author(s): Mohd. Amir, Vijay Kumar, Taj Mohammad, Ravins Dohare, Tabish Rehman, Mohamed F. Alajmi, Afzal Hussain, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1008543

PremPS: Predicting the impact of missense mutations on protein stability
Cited by: 93
Author(s): Yuting Chen, Haoyu Lu, Ning Zhang, Zefeng Zhu, Shuqin Wang, Minghui Li
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0233467

Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction
Cited by: 1
Author(s): Verónica Sáez-Jiménez, Željka Sanader Maršić, Matteo Lambrughi, Jae Ho Shin, Robin van Havere, Elena Papaleo, Lisbeth Olsson, Valeria Mapelli
Software Mentions: 1
Published: over 4 years ago

10.1016/j.celrep.2021.108984

Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies
Cited by: 21
Author(s): Charles D. Murin, Pavlo Gilchuk, Philipp A. Ilinykh, Kai Huang, Natalia Kuzmina, Xiaoli Shen, Jessica F. Bruhn, Aubrey L. Bryan, Edgar Davidson, Benjamin J. Doranz, Lauren E. Williamson, Jeffrey Copps, Tanwee Alkutkar, Andrew I. Flyak, Alexander Bukreyev, James E. Crowe, Andrew B. Ward
Software Mentions: 1
Published: over 3 years ago

10.1016/j.csbj.2020.01.002

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae
Cited by: 26
Author(s): Sundeep Chaitanya Vedithi, Carlos H M Rodrigues, Stephanie Portelli, Marcin J. Skwark, Madhusmita Das, David B. Ascher, Tom L. Blundell, Sony Malhotra
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.ejmech.2019.04.027

Synthesis and Structure–Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH
Cited by: 21
Author(s): Vinayak Singh, A. Pacitto, Stefano Donini, Davide M. Ferraris, Sándor Boros, Eszter Illyés, Bálint Szokol, Menico Rizzi, Tom L. Blundell, David B. Ascher, János Pató, Valerie Mizrahi
Software Mentions: 1
Published: over 5 years ago

10.1096/fj.201801956R

Receptor selectivity between the G proteins Gα 12 and Gα 13 is defined by a single leucine‐to‐isoleucine variation
Cited by: 18
Author(s): Amanda E. Mackenzie, Tezz Quon, Li Lin, Alexander S. Hauser, Laura Jenkins, Asuka Inoue, Andrew B. Tobin, David E. Gloriam, Brian D. Hudson, Graeme Milligan
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2020.00965

Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance
Cited by: 6
Author(s): Asma Munir, Sundeep Chaitanya Vedithi, Amanda K. Chaplin, Tom L. Blundell
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.575041

Structural Analysis of (p)ppGpp Reveals Its Versatile Binding Pattern for Diverse Types of Target Proteins
Cited by: 2
Author(s): G.S. Kushwaha, Anupam Patra, Neel Sarovar Bhavesh
Software Mentions: 1
Published: about 4 years ago

10.1074/jbc.RA117.000487

The N-terminal domain of a tick evasin is critical for chemokine binding and neutralization and confers specific binding activity to other evasins
Cited by: 20
Author(s): James R. O. Eaton, Yara Alenazi, Khushboo Singh, Graham Davies, Lucía Geis-Asteggiante, Benedikt M. Kessler, Carol V. Robinson, Akane Kawamura, Shoumo Bhattacharya
Software Mentions: 1
Published: over 6 years ago

10.1002/pro.3942

<scp>DynaMut2</scp>: Assessing changes in stability and flexibility upon single and multiple point missense mutations
Cited by: 177
Author(s): Carlos H M Rodrigues, Douglas E V Pires, David B. Ascher
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms20061337

Inhibition of Triple-Negative Breast Cancer Cell Aggressiveness by Cathepsin D Blockage: Role of Annexin A1
Cited by: 16
Author(s): Mariana Alves Pereira Zóia, Fernanda Van Petten de Vasconcelos Azevedo, Lara Vecchi, Sara Teixeira Soares Mota, Vinícius de Rezende Rodovalho, Antonielle Oliveira Cordeiro, Lucas Ian Veloso Correia, Anielle Christine Almeida Silva, Veridiana de Melo Rodrigues Ávila, Thaise Gonçalves Araújo, Luiz Ricardo Goulart
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22052415

Insights into Interactions between Interleukin-6 and Dendritic Polyglycerols
Cited by: 5
Author(s): Željka Sanader Maršić, Dušica Maysinger, Vlasta Bonačić‐Koutecký
Software Mentions: 1
Published: over 3 years ago

10.3390/antibiotics10070807

Molecular Analysis of Streptomycin Resistance Genes in Clinical Strains of Mycobacterium tuberculosis and Biocomputational Analysis of the MtGidB L101F Variant
Cited by: 6
Author(s): Álvaro Rodríguez-García, Rosa E. Mares‐Alejandre, Patricia L. A. Muñoz-Muñoz, Samuel Ruvalcaba-Ruiz, Ricardo González-Sánchez, Johanna Bernáldez-Sarabia, Samuel G. Meléndez-López, Alexei F. Licea-Navarro, Marco A. Ramos
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: Arpeggio

Papers Mentioning Arpeggio 39