A citation-based method for searching scientific literature

Giovanni Madeo, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio. J Mol Biol 2021
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


A combined transmembrane topology and signal peptide prediction method.
Lukas Käll, Anders Krogh, Erik L L Sonnhammer. J Mol Biol 2004
66

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.
Konstantinos D Tsirigos, Christoph Peters, Nanjiang Shu, Lukas Käll, Arne Elofsson. Nucleic Acids Res 2015
443
66

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
66


Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
Sikander Hayat, Christoph Peters, Nanjiang Shu, Konstantinos D Tsirigos, Arne Elofsson. Bioinformatics 2016
41
66

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
17
33

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
22
33

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

MEDUSA: Prediction of Protein Flexibility from Sequence.
Yann Vander Meersche, Gabriel Cretin, Alexandre G de Brevern, Jean-Christophe Gelly, Tatiana Galochkina. J Mol Biol 2021
11
33

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
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
14
33


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
3
33

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
5
33

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
33

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
7
33

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
6
33

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
38
33

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
6
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

Fast and accurate automatic structure prediction with HHpred.
Andrea Hildebrand, Michael Remmert, Andreas Biegert, Johannes Söding. Proteins 2009
306
33

ECOD: an evolutionary classification of protein domains.
Hua Cheng, R Dustin Schaeffer, Yuxing Liao, Lisa N Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V Grishin. PLoS Comput Biol 2014
163
33

Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase.
Armin Ruf, Tim Tetaz, Brigitte Schott, Catherine Joseph, Markus G Rudolph. Acta Crystallogr D Struct Biol 2016
3
33

The Structure and Topology of α-Helical Coiled Coils.
Andrei N Lupas, Jens Bassler, Stanislaw Dunin-Horkawicz. Subcell Biochem 2017
40
33


A census of protein repeats.
E M Marcotte, M Pellegrini, T O Yeates, D Eisenberg. J Mol Biol 1999
274
33

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva. J Mol Biol 2018
997
33


HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
33

Statistical density modification with non-crystallographic symmetry.
Thomas C Terwilliger. Acta Crystallogr D Biol Crystallogr 2002
40
33

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.
Manjunatha R Karpenahalli, Andrei N Lupas, Johannes Söding. BMC Bioinformatics 2007
146
33

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
33


New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins.
Daniel J Rigden, Duncan D Woodhead, Prudence W H Wong, Michael Y Galperin. PLoS One 2011
42
33

Use of non-crystallographic symmetry in protein structure refinement.
G J Kleywegt. Acta Crystallogr D Biol Crystallogr 1996
494
33

Hidden Markov model speed heuristic and iterative HMM search procedure.
L Steven Johnson, Sean R Eddy, Elon Portugaly. BMC Bioinformatics 2010
478
33

Finding Homologs in Amino Acid Sequences Using Network BLAST Searches.
Istvan Ladunga. Curr Protoc Bioinformatics 2017
5
33

Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.
M Remmert, A Biegert, D Linke, A N Lupas, J Söding. Mol Biol Evol 2010
71
33



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.