Zobrazeno 1 - 10
of 126
pro vyhledávání: '"Sameer Velankar"'
Autor:
Melanie Vollmar, Santosh Tirunagari, Deborah Harrus, David Armstrong, Romana Gáborová, Deepti Gupta, Marcelo Querino Lima Afonso, Genevieve Evans, Sameer Velankar
Publikováno v:
Scientific Data, Vol 11, Iss 1, Pp 1-18 (2024)
Abstract We present a novel system that leverages curators in the loop to develop a dataset and model for detecting structure features and functional annotations at residue-level from standard publication text. Our approach involves the integration o
Externí odkaz:
https://doaj.org/article/f80bdb22b3a741edbcfa948b5d5090f0
Autor:
Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Catherine L. Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H. W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
Publikováno v:
IUCrJ, Vol 11, Iss 2, Pp 140-151 (2024)
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, m
Externí odkaz:
https://doaj.org/article/0e43f020fe4a4894b6f5aa6a5fd3dc2f
Autor:
Joseph I. J. Ellaway, Stephen Anyango, Sreenath Nair, Hossam A. Zaki, Nurul Nadzirin, Harold R. Powell, Aleksandras Gutmanas, Mihaly Varadi, Sameer Velankar
Publikováno v:
Structural Dynamics, Vol 11, Iss 3, Pp 034701-034701-8 (2024)
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based st
Externí odkaz:
https://doaj.org/article/2f98abeaf372423c983a6288a14b7e31
Autor:
Sri Devan Appasamy, John Berrisford, Romana Gaborova, Sreenath Nair, Stephen Anyango, Sergei Grudinin, Mandar Deshpande, David Armstrong, Ivanna Pidruchna, Joseph I. J. Ellaway, Grisell Díaz Leines, Deepti Gupta, Deborah Harrus, Mihaly Varadi, Sameer Velankar
Publikováno v:
Scientific Data, Vol 10, Iss 1, Pp 1-13 (2023)
Abstract Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global
Externí odkaz:
https://doaj.org/article/d0756c17794b4f30a37d6a65e24cb126
Autor:
Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukas Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi, Sameer Velankar
Publikováno v:
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-11 (2023)
Abstract While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile to
Externí odkaz:
https://doaj.org/article/7838307f755a49408678c077b01f6d64
Autor:
Preeti Choudhary, Stephen Anyango, John Berrisford, James Tolchard, Mihaly Varadi, Sameer Velankar
Publikováno v:
Scientific Data, Vol 10, Iss 1, Pp 1-13 (2023)
Abstract More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorpor
Externí odkaz:
https://doaj.org/article/f525fdcb809742669e918419cf913c02
Autor:
Nicola Bordin, Ian Sillitoe, Vamsi Nallapareddy, Clemens Rauer, Su Datt Lam, Vaishali P. Waman, Neeladri Sen, Michael Heinzinger, Maria Littmann, Stephanie Kim, Sameer Velankar, Martin Steinegger, Burkhard Rost, Christine Orengo
Publikováno v:
Communications Biology, Vol 6, Iss 1, Pp 1-12 (2023)
A new protein domain classification protocol incorporating deep learning strategies for detecting sequence and structure similarities between domain is used to systematically study and analyse the predicted AlphaFold2 structural models for proteins o
Externí odkaz:
https://doaj.org/article/c077b0db693c4a798c9578aeecb33276
Autor:
Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango, Sameer Velankar
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-7 (2021)
Abstract Background Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (P
Externí odkaz:
https://doaj.org/article/7daf5eadd7f44940a4326a9042c318b1
Autor:
Gerard J. Kleywegt, Sameer Velankar
Publikováno v:
IUCrJ, Vol 9, Iss 4, Pp 399-400 (2022)
Externí odkaz:
https://doaj.org/article/fa21850392d44ea480baca9c46f03c0a
Autor:
David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koča, Radka Svobodová, Stephen K Burley, Alexander S Rose
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 10, p e1008247 (2020)
3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and
Externí odkaz:
https://doaj.org/article/313803daed7c480ca2e26869858d8f23