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



Times Cited
  Times     Co-cited
Similarity


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
7
50

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
12
50

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
4
50

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
2
50

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
50





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
6
50


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
2
50

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
4
50

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
3
50

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
4
50

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
23
50

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
1
100

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
1
100

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

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
50

Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
50

TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains?
Eitan Winter, Chris P Ponting. Trends Biochem Sci 2002
125
50

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding.
Bálint Mészáros, Gábor Erdos, Zsuzsanna Dosztányi. Nucleic Acids Res 2018
416
50


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
151
50


Structural basis for IL-12 and IL-23 receptor sharing reveals a gateway for shaping actions on T versus NK cells.
Caleb R Glassman, Yamuna Kalyani Mathiharan, Kevin M Jude, Leon Su, Ouliana Panova, Patrick J Lupardus, Jamie B Spangler, Lauren K Ely, Christoph Thomas, Georgios Skiniotis,[...]. Cell 2021
10
50


Protein interaction networks revealed by proteome coevolution.
Qian Cong, Ivan Anishchenko, Sergey Ovchinnikov, David Baker. Science 2019
56
50

IntFOLD: an integrated web resource for high performance protein structure and function prediction.
Liam J McGuffin, Recep Adiyaman, Ali H A Maghrabi, Ahmad N Shuid, Danielle A Brackenridge, John O Nealon, Limcy S Philomina. Nucleic Acids Res 2019
42
50

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.
Martin Steinegger, Milot Mirdita, Johannes Söding. Nat Methods 2019
42
50

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
860
50

The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
50

Towards automated crystallographic structure refinement with phenix.refine.
Pavel V Afonine, Ralf W Grosse-Kunstleve, Nathaniel Echols, Jeffrey J Headd, Nigel W Moriarty, Marat Mustyakimov, Thomas C Terwilliger, Alexandre Urzhumtsev, Peter H Zwart, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2012
50

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
50

Hidden Markov model speed heuristic and iterative HMM search procedure.
L Steven Johnson, Sean R Eddy, Elon Portugaly. BMC Bioinformatics 2010
439
50

Ab initio solution of macromolecular crystal structures without direct methods.
Airlie J McCoy, Robert D Oeffner, Antoni G Wrobel, Juha R M Ojala, Karl Tryggvason, Bernhard Lohkamp, Randy J Read. Proc Natl Acad Sci U S A 2017
26
50

Improved protein structure refinement guided by deep learning based accuracy estimation.
Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas, David Baker. Nat Commun 2021
27
50

Crystal structure of the catalytic domain of human ADAM33.
Peter Orth, Paul Reichert, Wenyan Wang, Winifred W Prosise, Taisa Yarosh-Tomaine, Gerald Hammond, Richard N Ingram, Li Xiao, Urooj A Mirza, Jun Zou,[...]. J Mol Biol 2004
65
50

Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations.
Seema R Lalani, Pengfei Liu, Jill A Rosenfeld, Levi B Watkin, Theodore Chiang, Magalie S Leduc, Wenmiao Zhu, Yan Ding, Shujuan Pan, Francesco Vetrini,[...]. Am J Hum Genet 2016
44
50

UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
303
50

MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
780
50

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs.
Brian Joseph Bender, Brennica Marlow, Jens Meiler. PLoS Comput Biol 2020
9
50


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.