A citation-based method for searching scientific literature

Yann Vander Meersche, Gabriel Cretin, Alexandre G de Brevern, Jean-Christophe Gelly, Tatiana Galochkina. J Mol Biol 2021
Times Cited: 8







List of co-cited articles
19 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
37

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
37

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
37


SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
37


PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks.
Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G de Brevern, Pierre Poulain. PeerJ 2017
17
25

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
314
25

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.
Yassine Ghouzam, Guillaume Postic, Pierre-Edouard Guerin, Alexandre G de Brevern, Jean-Christophe Gelly. Sci Rep 2016
22
25


HH-suite3 for fast remote homology detection and deep protein annotation.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
178
25



PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.
Gabriel Cretin, Tatiana Galochkina, Alexandre G de Brevern, Jean-Christophe Gelly. Int J Mol Sci 2021
2
100

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.
Michael Schantz Klausen, Martin Closter Jespersen, Henrik Nielsen, Kamilla Kjaergaard Jensen, Vanessa Isabell Jurtz, Casper Kaae Sønderby, Morten Otto Alexander Sommer, Ole Winther, Morten Nielsen, Bent Petersen,[...]. Proteins 2019
149
25


TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
25

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
25

QMEANDisCo-distance constraints applied on model quality estimation.
Gabriel Studer, Christine Rempfer, Andrew M Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. Bioinformatics 2020
152
25

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters.
Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin. J Mol Biol 2021
15
12

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive.
Yana Rose, Jose M Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S Rose, Sebastian Bittrich, Stephen K Burley,[...]. J Mol Biol 2021
20
12

PolarProtDb: A Database of Transmembrane and Secreted Proteins showing Apical-Basal Polarity.
András Zeke, László Dobson, Levente István Szekeres, Tamás Langó, Gábor E Tusnády. J Mol Biol 2021
2
50

aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals.
Federico Zambelli, Matteo Chiara, Erika Ferrandi, Pietro Mandreoli, Marco Antonio Tangaro, Giulio Pavesi, Graziano Pesole. J Mol Biol 2021
1
100

RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining.
Priyesh Agrawal, Sana Amir, Deepak, Drishtee Barua, Debasisa Mohanty. J Mol Biol 2021
5
20

BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins.
Giovanni Madeo, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio. J Mol Biol 2021
3
33





Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.
Andrew I Jewett, David Stelter, Jason Lambert, Shyam M Saladi, Otello M Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M Bashusqeh, Tom Keyes,[...]. J Mol Biol 2021
13
12


interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis.
Maria Filipa Pinto, Antonio Baici, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro, Annalisa Pastore, Fernando Rocha, Pedro M Martins. J Mol Biol 2021
2
50

FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity.
Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L L Sonnhammer. J Mol Biol 2021
4
25

MPTherm-pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.
A Kulandaisamy, Jan Zaucha, Dmitrij Frishman, M Michael Gromiha. J Mol Biol 2021
5
20

ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins.
R Prabakaran, Puneet Rawat, Sandeep Kumar, M Michael Gromiha. J Mol Biol 2021
5
20

ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases.
Wenliang Zhang, Binghui Zeng, Minglei Yang, Huan Yang, Jianbo Wang, Yongjie Deng, Haiyue Zhang, Guocai Yao, Song Wu, Weizhong Li. J Mol Biol 2021
5
20

ModFlex: Towards Function Focused Protein Modeling.
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik. J Mol Biol 2021
1
100

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.
Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A Andrade-Navarro. J Mol Biol 2021
1
100


FunRich enables enrichment analysis of OMICs datasets.
Pamali Fonseka, Mohashin Pathan, Sai V Chitti, Taeyoung Kang, Suresh Mathivanan. J Mol Biol 2021
36
12

Constrained Standardization of Count Data from Massive Parallel Sequencing.
Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg. J Mol Biol 2021
1
100

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.
Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes. J Mol Biol 2021
2
50

GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite.
Ruth Barshir, Simon Fishilevich, Tsippi Iny-Stein, Ofer Zelig, Yaron Mazor, Yaron Guan-Golan, Marilyn Safran, Doron Lancet. J Mol Biol 2021
3
33


geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome.
C Gómez-Martín, E Aparicio-Puerta, J M Medina, Guillermo Barturen, J L Oliver, M Hackenberg. J Mol Biol 2021
1
100

iPBA: a tool for protein structure comparison using sequence alignment strategies.
Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G de Brevern. Nucleic Acids Res 2011
57
12


Protein flexibility in the light of structural alphabets.
Pierrick Craveur, Agnel P Joseph, Jeremy Esque, Tarun J Narwani, Floriane Noël, Nicolas Shinada, Matthieu Goguet, Sylvain Leonard, Pierre Poulain, Olivier Bertrand,[...]. Front Mol Biosci 2015
46
12


svmPRAT: SVM-based protein residue annotation toolkit.
Huzefa Rangwala, Christopher Kauffman, George Karypis. BMC Bioinformatics 2009
21
12


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.