A citation-based method for searching scientific literature

A Kulandaisamy, Jan Zaucha, Dmitrij Frishman, M Michael Gromiha. J Mol Biol 2021
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
431
80

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations.
Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli. BMC Bioinformatics 2019
22
60

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.
Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis, Marianne Rooman. BMC Bioinformatics 2011
279
60

CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
362
60

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.
M Michael Gromiha, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, Akinori Sarai. Nucleic Acids Res 2002
41
60


Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine.
Tiziana Sanavia, Giovanni Birolo, Ludovica Montanucci, Paola Turina, Emidio Capriotti, Piero Fariselli. Comput Struct Biotechnol J 2020
25
60

Tracking cancer drugs in living cells by thermal profiling of the proteome.
Mikhail M Savitski, Friedrich B M Reinhard, Holger Franken, Thilo Werner, Maria Fälth Savitski, Dirk Eberhard, Daniel Martinez Molina, Rozbeh Jafari, Rebecca Bakszt Dovega, Susan Klaeger,[...]. Science 2014
461
40

ProTherm, version 4.0: thermodynamic database for proteins and mutants.
K Abdulla Bava, M Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai. Nucleic Acids Res 2004
235
40


Relationship between amino acid properties and protein stability: buried mutations.
M M Gromiha, M Oobatake, H Kono, H Uedaira, A Sarai. J Protein Chem 1999
49
40

Molecular mechanisms of disease-causing missense mutations.
Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R Panchenko, Emil Alexov. J Mol Biol 2013
140
40

MPTherm: database for membrane protein thermodynamics for understanding folding and stability.
A Kulandaisamy, R Sakthivel, M Michael Gromiha. Brief Bioinform 2021
3
66

MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
121
40

ProTherm: Thermodynamic Database for Proteins and Mutants.
M M Gromiha, J An, H Kono, M Oobatake, H Uedaira, A Sarai. Nucleic Acids Res 1999
89
40

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
323
40

Average assignment method for predicting the stability of protein mutants.
K Saraboji, M Michael Gromiha, M N Ponnuswamy. Biopolymers 2006
35
40

Large scale analysis of protein stability in OMIM disease related human protein variants.
Pier Luigi Martelli, Piero Fariselli, Castrense Savojardo, Giulia Babbi, Francesco Aggazio, Rita Casadio. BMC Genomics 2016
20
40

Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome.
Rita Casadio, Marco Vassura, Shalinee Tiwari, Piero Fariselli, Pier Luigi Martelli. Hum Mutat 2011
53
40

Physicochemical feature-based classification of amino acid mutations.
Bairong Shen, Jinwei Bai, Mauno Vihinen. Protein Eng Des Sel 2008
25
40

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
885
40


Modeling backbone flexibility improves protein stability estimation.
Shuangye Yin, Feng Ding, Nikolay V Dokholyan. Structure 2007
116
40

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
M D Shaji Kumar, K Abdulla Bava, M Michael Gromiha, Ponraj Prabakaran, Koji Kitajima, Hatsuho Uedaira, Akinori Sarai. Nucleic Acids Res 2006
256
40

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
40

A base measure of precision for protein stability predictors: structural sensitivity.
Octav Caldararu, Tom L Blundell, Kasper P Kepp. BMC Bioinformatics 2021
9
40

Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
49
40


9
40

PremPS: Predicting the impact of missense mutations on protein stability.
Yuting Chen, Haoyu Lu, Ning Zhang, Zefeng Zhu, Shuqin Wang, Minghui Li. PLoS Comput Biol 2020
24
40

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations.
Carlos H M Rodrigues, Douglas E V Pires, David B Ascher. Protein Sci 2021
33
40

INPS-MD: a web server to predict stability of protein variants from sequence and structure.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. Bioinformatics 2016
70
40

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
40



Systematic Investigation of the Data Set Dependency of Protein Stability Predictors.
Octav Caldararu, Rukmankesh Mehra, Tom L Blundell, Kasper P Kepp. J Chem Inf Model 2020
13
40

Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation.
Dinara R Usmanova, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, Alexander V Meister, Alisa G Yakupova, Fyodor A Kondrashov,[...]. Bioinformatics 2018
29
40

SDM--a server for predicting effects of mutations on protein stability and malfunction.
Catherine L Worth, Robert Preissner, Tom L Blundell. Nucleic Acids Res 2011
290
40

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years.
Rahul Nikam, A Kulandaisamy, K Harini, Divya Sharma, M Michael Gromiha. Nucleic Acids Res 2021
19
40

PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality.
Yang Yang, Siddhaling Urolagin, Abhishek Niroula, Xuesong Ding, Bairong Shen, Mauno Vihinen. Int J Mol Sci 2018
24
20


Catalytic inactivation of human phospholipase D2 by a naturally occurring Gly901Asp mutation.
Yoshiji Yamada, Yoshiko Banno, Hitoshi Yoshida, Ryosuke Kikuchi, Yukihiro Akao, Takashi Murate, Yoshinori Nozawa. Arch Med Res 2006
17
20



SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Jose M Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Martin, Sameer Velankar. Nucleic Acids Res 2019
58
20

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Stephen K Burley, Helen M Berman, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar. Methods Mol Biol 2017
206
20




Thermodynamic databases for proteins and protein-nucleic acid interactions.
A Sarai, M M Gromiha, J An, P Prabakaran, S Selvaraj, H Kono, M Oobatake, H Uedaira. Biopolymers 2001
14
20


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.