A citation-based method for searching scientific literature

Vincent Frappier, Matthieu Chartier, Rafael J Najmanovich. Nucleic Acids Res 2015
Times Cited: 92







List of co-cited articles
586 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
483
41

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
41

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
36


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
31

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
26


CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
386
21

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
19

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
18

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
16


UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
16


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
13

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
13



Performance of protein stability predictors.
Sofia Khan, Mauno Vihinen. Hum Mutat 2010
210
11


SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
10

A three-state prediction of single point mutations on protein stability changes.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio. BMC Bioinformatics 2008
221
10


MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
131
9

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
9


Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Hashem A Shihab, Julian Gough, David N Cooper, Peter D Stenson, Gary L A Barker, Keith J Edwards, Ian N M Day, Tom R Gaunt. Hum Mutat 2013
716
8

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
8


mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2017
68
11

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
8

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
8

Anisotropy of fluctuation dynamics of proteins with an elastic network model.
A R Atilgan, S R Durell, R L Jernigan, M C Demirel, O Keskin, I Bahar. Biophys J 2001
7

Eris: an automated estimator of protein stability.
Shuangye Yin, Feng Ding, Nikolay V Dokholyan. Nat Methods 2007
269
7

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell. J Mol Biol 2017
193
7


Predicting the functional effect of amino acid substitutions and indels.
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan. PLoS One 2012
7


Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
60
11

SIFT web server: predicting effects of amino acid substitutions on proteins.
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
7




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
6

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
9


MAESTROweb: a web server for structure-based protein stability prediction.
Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner. Bioinformatics 2016
69
8

MolProbity: all-atom structure validation for macromolecular crystallography.
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
6

The Amber biomolecular simulation programs.
David A Case, Thomas E Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J Woods. J Comput Chem 2005
6



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.