A citation-based method for searching scientific literature

Sofia Khan, Mauno Vihinen. Hum Mutat 2010
Times Cited: 210







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



Times Cited
  Times     Co-cited
Similarity



I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
976
49


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
295
33

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
32


mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
483
29

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
263
28

CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
386
25

A three-state prediction of single point mutations on protein stability changes.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio. BMC Bioinformatics 2008
221
24

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.
Yves Dehouck, Aline Grosfils, Benjamin Folch, Dimitri Gilis, Philippe Bogaerts, Marianne Rooman. Bioinformatics 2009
261
23

Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
60
38



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
306
21

MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
131
19

SDM: a server for predicting effects of mutations on protein stability.
Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B Ascher, Tom L Blundell. Nucleic Acids Res 2017
244
19



A method and server for predicting damaging missense mutations.
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
16

INPS: predicting the impact of non-synonymous variations on protein stability from sequence.
Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio. Bioinformatics 2015
66
24

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
15

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
35
42

Predicting free energy changes using structural ensembles.
Alexander Benedix, Caroline M Becker, Bert L de Groot, Amedeo Caflisch, Rainer A Böckmann. Nat Methods 2009
175
14

NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation.
Manuel Giollo, Alberto J M Martin, Ian Walsh, Carlo Ferrari, Silvio C E Tosatto. BMC Genomics 2014
69
20


Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability.
Manfred T Reetz, José D Carballeira, Andreas Vogel. Angew Chem Int Ed Engl 2006
286
13

VariBench: a benchmark database for variations.
Preethy Sasidharan Nair, Mauno Vihinen. Hum Mutat 2013
91
14


The stability effects of protein mutations appear to be universally distributed.
Nobuhiko Tokuriki, Francois Stricher, Joost Schymkowitz, Luis Serrano, Dan S Tawfik. J Mol Biol 2007
281
13



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
245
13

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
28
46

On the biases in predictions of protein stability changes upon variations: the INPS test case.
Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli. Bioinformatics 2019
23
56

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
407
13


Eris: an automated estimator of protein stability.
Shuangye Yin, Feng Ding, Nikolay V Dokholyan. Nat Methods 2007
269
12


iStable: off-the-shelf predictor integration for predicting protein stability changes.
Chi-Wei Chen, Jerome Lin, Yen-Wei Chu. BMC Bioinformatics 2013
109
12


How protein stability and new functions trade off.
Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S Tawfik. PLoS Comput Biol 2008
356
12

Stability effects of mutations and protein evolvability.
Nobuhiko Tokuriki, Dan S Tawfik. Curr Opin Struct Biol 2009
453
12

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
88
12


Performance of mutation pathogenicity prediction methods on missense variants.
Janita Thusberg, Ayodeji Olatubosun, Mauno Vihinen. Hum Mutat 2011
365
11

FoldX as Protein Engineering Tool: Better Than Random Based Approaches?
Oliver Buß, Jens Rudat, Katrin Ochsenreither. Comput Struct Biotechnol J 2018
76
14

Computational tools help improve protein stability but with a solubility tradeoff.
Aron Broom, Zachary Jacobi, Kyle Trainor, Elizabeth M Meiering. J Biol Chem 2017
58
18


Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins.
Tugba G Kucukkal, Marharyta Petukh, Lin Li, Emil Alexov. Curr Opin Struct Biol 2015
104
10


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.