Sameer Velankar

Affiliations
  • Protein Data Bank in Europe.

Publications (68)

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.

Briefings in bioinformatics
Avec: Vaishali P Waman , Neeladri Sen , Mihaly Varadi , Antoine Daina , Shoshana J Wodak , Vincent Zoete , Sameer Velankar , Christine Orengo

New restraints and validation approaches for nucleic acid structures in PDB-REDO.

Acta crystallographica. Section D, Structural biology
Avec: Ida de Vries , Tim Kwakman , Xiang Jun Lu , Maarten L Hekkelman , Mandar Deshpande , Sameer Velankar , Anastassis Perrakis , Robbie P Joosten

Highly accurate protein structure prediction for the human proteome.

Nature
Avec: Kathryn Tunyasuvunakool , Jonas Adler , Zachary Wu , Tim Green , Michal Zielinski , Augustin Žídek , Alex Bridgland , Andrew Cowie , Clemens Meyer , Agata Laydon , Sameer Velankar , Gerard J Kleywegt , Alex Bateman , Richard Evans , Alexander Pritzel , Michael Figurnov , Olaf Ronneberger , Russ Bates , Simon A A Kohl , Anna Potapenko , Andrew J Ballard , Bernardino Romera-Paredes , Stanislav Nikolov , Rishub Jain , Ellen Clancy , David Reiman , Stig Petersen , Andrew W Senior , Koray Kavukcuoglu , Ewan Birney , Pushmeet Kohli , John Jumper , Demis Hassabis

The CCP4 suite: integrative software for macromolecular crystallography.

Acta crystallographica. Section D, Structural biology
Avec: Jon Agirre , Mihaela Atanasova , Haroldas Bagdonas , Charles B Ballard , Arnaud Baslé , James Beilsten-Edmands , Rafael J Borges , David G Brown , J Javier Burgos-Mármol , John M Berrisford , Paul S Bond , Iracema Caballero , Lucrezia Catapano , Grzegorz Chojnowski , Atlanta G Cook , Kevin D Cowtan , Tristan I Croll , Judit É Debreczeni , Nicholas E Devenish , Eleanor J Dodson , Tarik R Drevon , Paul Emsley , Gwyndaf Evans , Phil R Evans , Maria Fando , James Foadi , Luis Fuentes-Montero , Elspeth F Garman , Markus Gerstel , Richard J Gildea , Kaushik Hatti , Maarten L Hekkelman , Philipp Heuser , Soon Wen Hoh , Michael A Hough , Huw T Jenkins , Elisabet Jiménez , Robbie P Joosten , Ronan M Keegan , Nicholas Keep , Eugene B Krissinel , Petr Kolenko , Oleg Kovalevskiy , Victor S Lamzin , David M Lawson , Andrey A Lebedev , Andrew G W Leslie , Bernhard Lohkamp , Fei Long , Martin Malý , Airlie J McCoy , Stuart J McNicholas , Ana Medina , Claudia Millán , James W Murray , Garib N Murshudov , Robert A Nicholls , Martin E M Noble , Robert Oeffner , Navraj S Pannu , James M Parkhurst , Nicholas Pearce , Joana Pereira , Anastassis Perrakis , Harold R Powell , Randy J Read , Daniel J Rigden , William Rochira , Massimo Sammito , Filomeno Sánchez Rodríguez , George M Sheldrick , Kathryn L Shelley , Felix Simkovic , Adam J Simpkin , Pavol Skubak , Egor Sobolev , Roberto A Steiner , Kyle Stevenson , Ivo Tews , Jens M H Thomas , Andrea Thorn , Josep Triviño Valls , Ville Uski , Isabel Usón , Alexei Vagin , Sameer Velankar , Melanie Vollmar , Helen Walden , David Waterman , Keith S Wilson , Martyn D Winn , Graeme Winter , Marcin Wojdyr , Keitaro Yamashita

Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership.

Acta crystallographica. Section D, Structural biology
Avec: Wenqing Xu , Sameer Velankar , Ardan Patwardhan , Jeffrey C Hoch , Stephen K Burley , Genji Kurisu

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank.

bioRxiv : the preprint server for biology
Avec: Kumaran Baskaran , Eliza Ploskon , Roberto Tejero , Masashi Yokochi , Deborah Harrus , Yuhe Liang , Ezra Peisach , Irina Persikova , Theresa A Ramelot , Monica Sekharan , James Tolchard , John D Westbrook , Benjamin Bardiaux , Charles D Schwieters , Ardan Patwardhan , Sameer Velankar , Stephen K Burley , Genji Kurisu , Jeffrey C Hoch , Gaetano T Montelione , Geerten W Vuister , Jasmine Y Young

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.

Scientific data
Avec: 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

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.

Journal of molecular biology
Avec: Brinda Vallat , Benjamin M Webb , John D Westbrook , Thomas D Goddard , Christian A Hanke , Andrea Graziadei , Ezra Peisach , Arthur Zalevsky , Jared Sagendorf , Hongsuda Tangmunarunkit , Serban Voinea , Monica Sekharan , Jian Yu , Alexander A M J J Bonvin , Frank DiMaio , Gerhard Hummer , Jens Meiler , Emad Tajkhorshid , Thomas E Ferrin , Catherine L Lawson , Alexander Leitner , Juri Rappsilber , Claus A M Seidel , Cy M Jeffries , Stephen K Burley , Jeffrey C Hoch , Genji Kurisu , Kyle Morris , Ardan Patwardhan , Sameer Velankar , Torsten Schwede , Jill Trewhella , Carl Kesselman , Helen M Berman , Andrej Sali

Flat, wrinkled, or ridged: Relaxation of an elastic film on a viscous substrate undergoing continuous compression.

International journal of solids and structures
Avec: Xianheng Guan , Nhung Nguyen , Luka Pocivavsek , Enrique Cerda , Sachin Velankar

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies.

Structural dynamics (Melville, N.Y.)
Avec: Joseph I J Ellaway , Stephen Anyango , Sreenath Nair , Hossam A Zaki , Nurul Nadzirin , Harold R Powell , Aleksandras Gutmanas , Mihaly Varadi , Sameer Velankar

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

Structure (London, England : 1993)
Avec: Zukang Feng , John D Westbrook , Raul Sala , Oliver S Smart , Gérard Bricogne , Masaaki Matsubara , Issaku Yamada , Shinichiro Tsuchiya , Kiyoko F Aoki-Kinoshita , Jeffrey C Hoch , Genji Kurisu , Sameer Velankar , Stephen K Burley , Jasmine Y Young

High-performance macromolecular data delivery and visualization for the web.

Acta crystallographica. Section D, Structural biology
Avec: David Sehnal , Radka Svobodová , Karel Berka , Alexander S Rose , Stephen K Burley , Sameer Velankar , Jaroslav Koča

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

Nucleic acids research
Avec: David Sehnal , Sebastian Bittrich , Mandar Deshpande , Radka Svobodová , Karel Berka , Václav Bazgier , Sameer Velankar , Stephen K Burley , Jaroslav Koča , Alexander S Rose

Caveolin-1 mediates soft scaffold-enhanced adipogenesis of human mesenchymal stem cells.

Stem cell research & therapy
Avec: Shiqi Xiang , Zhong Li , Madalyn R Fritch , La Li , Sachin Velankar , Yuwei Liu , Jihee Sohn , Natasha Baker , Hang Lin , Rocky S Tuan

The impact of AlphaFold Protein Structure Database on the fields of life sciences.

Proteomics
Avec: Mihaly Varadi , Sameer Velankar

Clustering predicted structures at the scale of the known protein universe.

Nature
Avec: Inigo Barrio-Hernandez , Jingi Yeo , Jürgen Jänes , Milot Mirdita , Cameron L M Gilchrist , Tanita Wein , Mihaly Varadi , Sameer Velankar , Pedro Beltrao , Martin Steinegger

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Proteins
Avec: Marc F Lensink , Guillaume Brysbaert , Nessim Raouraoua , Paul A Bates , Marco Giulini , Rodrigo V Honorato , Charlotte van Noort , Joao M C Teixeira , Alexandre M J J Bonvin , Ren Kong , Hang Shi , Xufeng Lu , Shan Chang , Jian Liu , Zhiye Guo , Xiao Chen , Alex Morehead , Raj S Roy , Tianqi Wu , Nabin Giri , Farhan Quadir , Chen Chen , Jianlin Cheng , Carlos A Del Carpio , Eichiro Ichiishi , Luis A Rodriguez-Lumbreras , Juan Fernandez-Recio , Ameya Harmalkar , Lee-Shin Chu , Sam Canner , Rituparna Smanta , Jeffrey J Gray , Hao Li , Peicong Lin , Jiahua He , Huanyu Tao , Sheng-You Huang , Jorge Roel-Touris , Brian Jimenez-Garcia , Charles W Christoffer , Anika J Jain , Yuki Kagaya , Harini Kannan , Tsukasa Nakamura , Genki Terashi , Jacob C Verburgt , Yuanyuan Zhang , Zicong Zhang , Hayato Fujuta , Masakazu Sekijima , Daisuke Kihara , Omeir Khan , Sergei Kotelnikov , Usman Ghani , Dzmitry Padhorny , Dmitri Beglov , Sandor Vajda , Dima Kozakov , Surendra S Negi , Tiziana Ricciardelli , Didier Barradas-Bautista , Zhen Cao , Mohit Chawla , Luigi Cavallo , Romina Oliva , Rui Yin , Melyssa Cheung , Johnathan D Guest , Jessica Lee , Brian G Pierce , Ben Shor , Tomer Cohen , Matan Halfon , Dina Schneidman-Duhovny , Shaowen Zhu , Rujie Yin , Yuanfei Sun , Yang Shen , Martyna Maszota-Zieleniak , Krzysztof K Bojarski , Emilia A Lubecka , Mateusz Marcisz , Annemarie Danielsson , Lukasz Dziadek , Margrethe Gaardlos , Artur Gieldon , Adam Liwo , Sergey A Samsonov , Rafal Slusarz , Karolina Zieba , Adam K Sieradzan , Cezary Czaplewski , Shinpei Kobayashi , Yuta Miyakawa , Yasuomi Kiyota , Mayuko Takeda-Shitaka , Kliment Olechnovic , Lukas Valancauskas , Justas Dapkunas , Ceslovas Venclovas , Bjorn Wallner , Lin Yang , Chengyu Hou , Xiaodong He , Shuai Guo , Shenda Jiang , Xiaoliang Ma , Rui Duan , Liming Qui , Xianjin Xu , Xiaoqin Zou , Sameer Velankar , Shoshana J Wodak

Challenges in bridging the gap between protein structure prediction and functional interpretation.

Proteins
Avec: Mihaly Varadi , Maxim Tsenkov , Sameer Velankar

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

Journal of cheminformatics
Avec: Ibrahim Roshan Kunnakkattu , Preeti Choudhary , Lukas Pravda , Nurul Nadzirin , Oliver S Smart , Qi Yuan , Stephen Anyango , Sreenath Nair , Mihaly Varadi , Sameer Velankar

Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature.

Scientific data
Avec: Melanie Vollmar , Santosh Tirunagari , Deborah Harrus , David Armstrong , Romana Gáborová , Deepti Gupta , Marcelo Querino Lima Afonso , Genevieve Evans , Sameer Velankar

Finding enzyme cofactors in Protein Data Bank.

Bioinformatics (Oxford, England)
Avec: Abhik Mukhopadhyay , Neera Borkakoti , Lukáš Pravda , Jonathan D Tyzack , Janet M Thornton , Sameer Velankar

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.

Nucleic acids research
Avec: Ian Sillitoe , Antonina Andreeva , Tom L Blundell , Daniel W A Buchan , Robert D Finn , Julian Gough , David Jones , Lawrence A Kelley , Typhaine Paysan-Lafosse , Su Datt Lam , Alexey G Murzin , Arun Prasad Pandurangan , Gustavo A Salazar , Marcin J Skwark , Michael J E Sternberg , Sameer Velankar , Christine Orengo

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).

F1000Research
Avec: Christine Orengo , Sameer Velankar , Shoshana Wodak , Vincent Zoete , Alexandre M J J Bonvin , Arne Elofsson , K Anton Feenstra , Dietland L Gerloff , Thomas Hamelryck , John M Hancock , Manuela Helmer-Citterich , Adam Hospital , Modesto Orozco , Anastassis Perrakis , Matthias Rarey , Claudio Soares , Joel L Sussman , Janet M Thornton , Pierre Tuffery , Gabor Tusnady , Rikkert Wierenga , Tiina Salminen , Bohdan Schneider

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Nucleic acids research
Avec: Mihaly Varadi , Stephen Anyango , Mandar Deshpande , Sreenath Nair , Cindy Natassia , Galabina Yordanova , David Yuan , Oana Stroe , Gemma Wood , Agata Laydon , Augustin Žídek , Tim Green , Kathryn Tunyasuvunakool , Stig Petersen , John Jumper , Ellen Clancy , Richard Green , Ankur Vora , Mira Lutfi , Michael Figurnov , Andrew Cowie , Nicole Hobbs , Pushmeet Kohli , Gerard Kleywegt , Ewan Birney , Demis Hassabis , Sameer Velankar

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

Bioinformatics (Oxford, England)
Avec: Sreenath Nair , Mihály Váradi , Nurul Nadzirin , Lukáš Pravda , Stephen Anyango , Saqib Mir , John Berrisford , David Armstrong , Aleksandras Gutmanas , Sameer Velankar

PDBeCIF: an open-source mmCIF/CIF parsing and processing package.

BMC bioinformatics
Avec: Glen van Ginkel , Lukáš Pravda , José M Dana , Mihaly Varadi , Peter Keller , Stephen Anyango , Sameer Velankar

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.

Journal of molecular biology
Avec: John D Westbrook , Jasmine Y Young , Chenghua Shao , Zukang Feng , Vladimir Guranovic , Catherine L Lawson , Brinda Vallat , Paul D Adams , John M Berrisford , Gerard Bricogne , Kay Diederichs , Robbie P Joosten , Peter Keller , Nigel W Moriarty , Oleg V Sobolev , Sameer Velankar , Clemens Vonrhein , David G Waterman , Genji Kurisu , Helen M Berman , Stephen K Burley , Ezra Peisach

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

Database : the journal of biological databases and curation
Avec: Preeti Choudhary , Zukang Feng , John Berrisford , Henry Chao , Yasuyo Ikegawa , Ezra Peisach , Dennis W Piehl , James Smith , Ahsan Tanweer , Mihaly Varadi , John D Westbrook , Jasmine Y Young , Ardan Patwardhan , Kyle L Morris , Jeffrey C Hoch , Genji Kurisu , Sameer Velankar , Stephen K Burley

Harnessing the 3D-Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data.

Current protocols
Avec: Paulyna Magaña , Sreenath Nair , Mihaly Varadi , Sameer Velankar

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

Protein science : a publication of the Protein Society
Avec: Mihaly Varadi , Stephen Anyango , Sri Devan Appasamy , David Armstrong , Marcus Bage , John Berrisford , Preeti Choudhary , Damian Bertoni , Mandar Deshpande , Grisell Diaz Leines , Joseph Ellaway , Genevieve Evans , Romana Gaborova , Deepti Gupta , Aleksandras Gutmanas , Deborah Harrus , Gerard J Kleywegt , Weslley Morellato Bueno , Nurul Nadzirin , Sreenath Nair , Lukas Pravda , Marcelo Querino Lima Afonso , David Sehnal , Ahsan Tanweer , James Tolchard , Charlotte Abrams , Roisin Dunlop , Sameer Velankar

Community recommendations on cryoEM data archiving and validation.

IUCrJ
Avec: 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

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Structure (London, England : 1993)
Avec: Helen M Berman , Paul D Adams , Alexandre A Bonvin , Stephen K Burley , Bridget Carragher , Wah Chiu , Frank DiMaio , Thomas E Ferrin , Margaret J Gabanyi , Thomas D Goddard , Patrick R Griffin , Juergen Haas , Christian A Hanke , Jeffrey C Hoch , Gerhard Hummer , Genji Kurisu , Catherine L Lawson , Alexander Leitner , John L Markley , Jens Meiler , Gaetano T Montelione , George N Phillips , Thomas Prisner , Juri Rappsilber , David C Schriemer , Torsten Schwede , Claus A M Seidel , Timothy S Strutzenberg , Dmitri I Svergun , Emad Tajkhorshid , Jill Trewhella , Brinda Vallat , Sameer Velankar , Geerten W Vuister , Benjamin Webb , John D Westbrook , Kate L White , Andrej Sali

Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition.

Proteins
Avec: Marc F Lensink , Nurul Nadzirin , Sameer Velankar , Shoshana J Wodak

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Proteins
Avec: Marc F Lensink , Guillaume Brysbaert , Nurul Nadzirin , Sameer Velankar , Raphaël A G Chaleil , Tereza Gerguri , Paul A Bates , Elodie Laine , Alessandra Carbone , Sergei Grudinin , Ren Kong , Ran-Ran Liu , Xi-Ming Xu , Hang Shi , Shan Chang , Miriam Eisenstein , Agnieszka Karczynska , Cezary Czaplewski , Emilia Lubecka , Agnieszka Lipska , Paweł Krupa , Magdalena Mozolewska , Łukasz Golon , Sergey Samsonov , Adam Liwo , Silvia Crivelli , Guillaume Pagès , Mikhail Karasikov , Maria Kadukova , Yumeng Yan , Sheng-You Huang , Mireia Rosell , Luis A Rodríguez-Lumbreras , Miguel Romero-Durana , Lucía Díaz-Bueno , Juan Fernandez-Recio , Charles Christoffer , Genki Terashi , Woong-Hee Shin , Tunde Aderinwale , Sai Raghavendra Maddhuri Venkata Subraman , Daisuke Kihara , Dima Kozakov , Sandor Vajda , Kathryn Porter , Dzmitry Padhorny , Israel Desta , Dmitri Beglov , Mikhail Ignatov , Sergey Kotelnikov , Iain H Moal , David W Ritchie , Isaure Chauvot de Beauchêne , Bernard Maigret , Marie-Dominique Devignes , Maria E Ruiz Echartea , Didier Barradas-Bautista , Zhen Cao , Luigi Cavallo , Romina Oliva , Yue Cao , Yang Shen , Minkyung Baek , Taeyong Park , Hyeonuk Woo , Chaok Seok , Merav Braitbard , Lirane Bitton , Dina Scheidman-Duhovny , Justas Dapkūnas , Kliment Olechnovič , Česlovas Venclovas , Petras J Kundrotas , Saveliy Belkin , Devlina Chakravarty , Varsha D Badal , Ilya A Vakser , Thom Vreven , Sweta Vangaveti , Tyler Borrman , Zhiping Weng , Johnathan D Guest , Ragul Gowthaman , Brian G Pierce , Xianjin Xu , Rui Duan , Liming Qiu , Jie Hou , Benjamin Ryan Merideth , Zhiwei Ma , Jianlin Cheng , Xiaoqin Zou , Panagiotis I Koukos , Jorge Roel-Touris , Francesco Ambrosetti , Cunliang Geng , Jörg Schaarschmidt , Mikael E Trellet , Adrien S J Melquiond , Li Xue , Brian Jiménez-García , Charlotte W van Noort , Rodrigo V Honorato , Alexandre M J J Bonvin , Shoshana J Wodak

PDBe: improved findability of macromolecular structure data in the PDB.

Nucleic acids research
Avec: David R Armstrong , John M Berrisford , Matthew J Conroy , Aleksandras Gutmanas , Stephen Anyango , Preeti Choudhary , Alice R Clark , Jose M Dana , Mandar Deshpande , Roisin Dunlop , Paul Gane , Romana Gáborová , Deepti Gupta , Pauline Haslam , Jaroslav Koča , Lora Mak , Saqib Mir , Abhik Mukhopadhyay , Nurul Nadzirin , Sreenath Nair , Typhaine Paysan-Lafosse , Lukas Pravda , David Sehnal , Osman Salih , Oliver Smart , James Tolchard , Mihaly Varadi , Radka Svobodova-Vařeková , Hossam Zaki , Gerard J Kleywegt , Sameer Velankar

Tuning of thermoresponsive pNIPAAm hydrogels for the topical retention of controlled release ocular therapeutics.

Journal of materials chemistry. B
Avec: Elena Bellotti , Morgan V Fedorchak , Sachin Velankar , Steven R Little

Interfacially compatibilized PI/PDMS blends with reduced octadecylamine-functionalized graphene oxide: morphological and rheological properties.

Soft matter
Avec: Jaber Nasrollah Gavgani , Fatemeh Goharpey , Sachin Velankar

High-performance macromolecular data delivery and visualization for the web. Corrigendum.

Acta crystallographica. Section D, Structural biology
Avec: David Sehnal , Radka Svobodová , Karel Berka , Alexander S Rose , Stephen K Burley , Sameer Velankar , Jaroslav Koča

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Glycobiology
Avec: Chenghua Shao , Zukang Feng , John D Westbrook , Ezra Peisach , John Berrisford , Yasuyo Ikegawa , Genji Kurisu , Sameer Velankar , Stephen K Burley , Jasmine Y Young

The Protein Data Bank Archive.

Methods in molecular biology (Clifton, N.J.)
Avec: Sameer Velankar , Stephen K Burley , Genji Kurisu , Jeffrey C Hoch , John L Markley

Dynamic Luminal Topography: A Potential Strategy to Prevent Vascular Graft Thrombosis.

Frontiers in bioengineering and biotechnology
Avec: Nandan N Nath , Luka Pocivavsek , Joseph A Pugar , Ya Gao , Karim Salem , Nandan Pitre , Ryan McEnaney , Sachin Velankar , Edith Tzeng

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

Proteins
Avec: Marc F Lensink , Guillaume Brysbaert , Théo Mauri , Nurul Nadzirin , Sameer Velankar , Raphael A G Chaleil , Tereza Clarence , Paul A Bates , Ren Kong , Bin Liu , Guangbo Yang , Ming Liu , Hang Shi , Xufeng Lu , Shan Chang , Raj S Roy , Farhan Quadir , Jian Liu , Jianlin Cheng , Anna Antoniak , Cezary Czaplewski , Artur Giełdoń , Mateusz Kogut , Agnieszka G Lipska , Adam Liwo , Emilia A Lubecka , Martyna Maszota-Zieleniak , Adam K Sieradzan , Rafał Ślusarz , Patryk A Wesołowski , Karolina Zięba , Carlos A Del Carpio Muñoz , Eiichiro Ichiishi , Ameya Harmalkar , Jeffrey J Gray , Alexandre M J J Bonvin , Francesco Ambrosetti , Rodrigo Vargas Honorato , Zuzana Jandova , Brian Jiménez-García , Panagiotis I Koukos , Siri Van Keulen , Charlotte W Van Noort , Manon Réau , Jorge Roel-Touris , Sergei Kotelnikov , Dzmitry Padhorny , Kathryn A Porter , Andrey Alekseenko , Mikhail Ignatov , Israel Desta , Ryota Ashizawa , Zhuyezi Sun , Usman Ghani , Nasser Hashemi , Sandor Vajda , Dima Kozakov , Mireia Rosell , Luis A Rodríguez-Lumbreras , Juan Fernandez-Recio , Agnieszka Karczynska , Sergei Grudinin , Yumeng Yan , Hao Li , Peicong Lin , Sheng-You Huang , Charles Christoffer , Genki Terashi , Jacob Verburgt , Daipayan Sarkar , Tunde Aderinwale , Xiao Wang , Daisuke Kihara , Tsukasa Nakamura , Yuya Hanazono , Ragul Gowthaman , Johnathan D Guest , Rui Yin , Ghazaleh Taherzadeh , Brian G Pierce , Didier Barradas-Bautista , Zhen Cao , Luigi Cavallo , Romina Oliva , Yuanfei Sun , Shaowen Zhu , Yang Shen , Taeyong Park , Hyeonuk Woo , Jinsol Yang , Sohee Kwon , Jonghun Won , Chaok Seok , Yasuomi Kiyota , Shinpei Kobayashi , Yoshiki Harada , Mayuko Takeda-Shitaka , Petras J Kundrotas , Amar Singh , Ilya A Vakser , Justas Dapkūnas , Kliment Olechnovič , Česlovas Venclovas , Rui Duan , Liming Qiu , Xianjin Xu , Shuang Zhang , Xiaoqin Zou , Shoshana J Wodak

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.

Briefings in bioinformatics
Avec: Neeladri Sen , Ivan Anishchenko , Nicola Bordin , Ian Sillitoe , Sameer Velankar , David Baker , Christine Orengo

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.

Nucleic acids research
Avec: Mihaly Varadi , Damian Bertoni , Paulyna Magana , Urmila Paramval , Ivanna Pidruchna , Malarvizhi Radhakrishnan , Maxim Tsenkov , Sreenath Nair , Milot Mirdita , Jingi Yeo , Oleg Kovalevskiy , Kathryn Tunyasuvunakool , Agata Laydon , Augustin Žídek , Hamish Tomlinson , Dhavanthi Hariharan , Josh Abrahamson , Tim Green , John Jumper , Ewan Birney , Martin Steinegger , Demis Hassabis , Sameer Velankar

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Nucleic acids research
Avec: Matthew Thakur , Alex Bateman , Cath Brooksbank , Mallory Freeberg , Melissa Harrison , Matthew Hartley , Thomas Keane , Gerard Kleywegt , Andrew Leach , Mariia Levchenko , Sarah Morgan , Ellen M McDonagh , Sandra Orchard , Irene Papatheodorou , Sameer Velankar , Juan Antonio Vizcaino , Rick Witham , Barbara Zdrazil , Johanna McEntyre

Topographic de-adhesion in the viscoelastic limit.

Journal of the Royal Society, Interface
Avec: Nhung Nguyen , Eugenio Hamm Hahn , Sachin Velankar , Enrique Cerda , Luka Pocivavsek

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

Journal of molecular biology
Avec: Brinda Vallat , Gerardo Tauriello , Stefan Bienert , Juergen Haas , Benjamin M Webb , Augustin Žídek , Wei Zheng , Ezra Peisach , Dennis W Piehl , Ivan Anischanka , Ian Sillitoe , James Tolchard , Mihaly Varadi , David Baker , Christine Orengo , Yang Zhang , Jeffrey C Hoch , Genji Kurisu , Ardan Patwardhan , Sameer Velankar , Stephen K Burley , Andrej Sali , Torsten Schwede , Helen M Berman , John D Westbrook

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.

Current opinion in structural biology
Avec: Mihaly Varadi , Nicola Bordin , Christine Orengo , Sameer Velankar

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit.

Current protocols
Avec: Sebastian Bittrich , Adam Midlik , Mihaly Varadi , Sameer Velankar , Stephen K Burley , Jasmine Y Young , David Sehnal , Brinda Vallat

Automatic annotation of protein residues in published papers.

Acta crystallographica. Section F, Structural biology communications
Avec: Robert Firth , Francesco Talo , Aravind Venkatesan , Abhik Mukhopadhyay , Johanna McEntyre , Sameer Velankar , Chris Morris

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.

Nucleic acids research
Avec: Jose M Dana , Aleksandras Gutmanas , Nidhi Tyagi , Guoying Qi , Claire O'Donovan , Maria Martin , Sameer Velankar

Active wrinkles to drive self-cleaning: A strategy for anti-thrombotic surfaces for vascular grafts.

Biomaterials
Avec: Luka Pocivavsek , Sang-Ho Ye , Joseph Pugar , Edith Tzeng , Enrique Cerda , Sachin Velankar , William R Wagner

West-Life: A Virtual Research Environment for structural biology.

Journal of structural biology: X
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Self-assembly of multiscale anisotropic hydrogels through interfacial polyionic complexation.

Journal of biomedical materials research. Part A
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BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.

PLoS computational biology
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Improved chemosensitivity following mucolytic therapy in patient-derived models of mucinous appendix cancer.

Translational research : the journal of laboratory and clinical medicine
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Design of Thermoresponsive Polyamine Cross-Linked Perfluoropolyether Hydrogels for Imaging and Delivery Applications.

ACS medicinal chemistry letters
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Community recommendations on cryoEM data archiving and validation.

ArXiv
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PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization.

Bioinformatics (Oxford, England)
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Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.

Structure (London, England : 1993)
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Whither structural biologists?

IUCrJ
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A structural biology community assessment of AlphaFold2 applications.

Nature structural & molecular biology
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3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.

GigaScience
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AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms.

Communications biology
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Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.

Scientific data
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EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

Nucleic acids research
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Evaluation of the External Rotation of the Femur Component in Functionally Aligned Robotic-Assisted Total Knee Arthroplasty.

Cureus
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Minimized Soft Tissue Release in Robotic-Assisted Total Knee Arthroplasty: A Retrospective Review of 100 Cases.

Cureus
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Réseau de co-auteurs

Mihaly Varadi 21 collaborations
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