A citation-based method for searching scientific literature

Md Arifuzzaman, Sarmistha Mitra, Raju Das, Amir Hamza, Nurul Absar, Raju Dash. Ann Hum Genet 2020
Times Cited: 11







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



Times Cited
  Times     Co-cited
Similarity


Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene.
S M Zahid Hosen, Raju Dash, Md Junaid, Sarmistha Mitra, Nurul Absar. Comput Biol Chem 2019
13
63

Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient.
Raju Dash, Md Junaid, Sarmistha Mitra, Md Arifuzzaman, S M Zahid Hosen. J Mol Model 2019
20
54

Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1.
Raju Dash, Md Arifuzzaman, Sarmistha Mitra, Md Abdul Hannan, Nurul Absar, S M Zahid Hosen. Curr Pharm Des 2019
10
60




New ways to boost molecular dynamics simulations.
Elmar Krieger, Gert Vriend. J Comput Chem 2015
379
36

Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding.
Raju Dash, Md Chayan Ali, Nayan Dash, Md Abul Kalam Azad, S M Zahid Hosen, Md Abdul Hannan, Il Soo Moon. Int J Mol Sci 2019
20
36

Bio3d: an R package for the comparative analysis of protein structures.
Barry J Grant, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves. Bioinformatics 2006
937
36

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
36

Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA.
Himani Tanwar, D Thirumal Kumar, C George Priya Doss, Hatem Zayed. Metab Brain Dis 2019
13
36


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
36

Fast empirical pKa prediction by Ewald summation.
Elmar Krieger, Jens E Nielsen, Chris A E M Spronk, Gert Vriend. J Mol Graph Model 2006
224
27


PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky. PLoS Comput Biol 2014
396
27



Making optimal use of empirical energy functions: force-field parameterization in crystal space.
Elmar Krieger, Tom Darden, Sander B Nabuurs, Alexei Finkelstein, Gert Vriend. Proteins 2004
586
27


Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.
Elmar Krieger, Roland L Dunbrack, Rob W W Hooft, Barbara Krieger. Methods Mol Biol 2012
116
27

The energy landscapes and motions of proteins.
H Frauenfelder, S G Sligar, P G Wolynes. Science 1991
27

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
27

YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations.
Henrik Land, Maria Svedendahl Humble. Methods Mol Biol 2018
139
27

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
27

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
27

Convergence of sampling in protein simulations.
Berk Hess. Phys Rev E Stat Nonlin Soft Matter Phys 2002
286
27


CADD: predicting the deleteriousness of variants throughout the human genome.
Philipp Rentzsch, Daniela Witten, Gregory M Cooper, Jay Shendure, Martin Kircher. Nucleic Acids Res 2019
27

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
27

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.
Karthik A Jagadeesh, Aaron M Wenger, Mark J Berger, Harendra Guturu, Peter D Stenson, David N Cooper, Jonathan A Bernstein, Gill Bejerano. Nat Genet 2016
429
27


N-Acetyl-D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration.
Md Ariful Islam, Ho Jin Choi, Raju Dash, Syeda Ridita Sharif, Diyah Fatimah Oktaviani, Dae-Hyun Seog, Il Soo Moon. Int J Mol Sci 2020
3
100

N-acetyl-D-glucosamine kinase binds dynein light chain roadblock 1 and promotes protein aggregate clearance.
Md Kamal Hossain Ripon, HyunSook Lee, Raju Dash, Ho Jin Choi, Diyah Fatimah Oktaviani, Il Soo Moon, Md Nazmul Haque. Cell Death Dis 2020
6
50

Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter.
Raju Dash, Md Chayan Ali, Md Liton Rana, Yeasmin Akter Munni, Largess Barua, Israt Jahan, Mst Fatema Haque, Md Abdul Hannan, Il Soo Moon. Int J Mol Sci 2020
11
27


Toll-like receptor signaling pathways.
Takumi Kawasaki, Taro Kawai. Front Immunol 2014
18

Prediction of drug solubility from structure.
William L Jorgensen, Erin M Duffy. Adv Drug Deliv Rev 2002
401
18


KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
18

The Alzheimer's disease beta-secretase enzyme, BACE1.
Sarah L Cole, Robert Vassar. Mol Neurodegener 2007
302
18

Design and nuclear magnetic resonance (NMR) structure determination of the second extracellular immunoglobulin tyrosine kinase A (TrkAIg2) domain construct for binding site elucidation in drug discovery.
Debbie K Shoemark, Christopher Williams, Mark S Fahey, Judy J Watson, Sue J Tyler, Simon J Scoltock, Rosamund Z Ellis, Elaine Wickenden, Antony J Burton, Jennifer L Hemmings,[...]. J Med Chem 2015
5
40



Molecular basis of neurotrophin-receptor interactions.
Mookda Pattarawarapan, Kevin Burgess. J Med Chem 2003
54
18


Lipid14: The Amber Lipid Force Field.
Callum J Dickson, Benjamin D Madej, Age A Skjevik, Robin M Betz, Knut Teigen, Ian R Gould, Ross C Walker. J Chem Theory Comput 2014
723
18

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
18

A Computational workflow for the identification of the potent inhibitor of type II secretion system traffic ATPase of Pseudomonas aeruginosa.
Md Arifuzzaman, Sarmistha Mitra, Sultana Israt Jahan, Md Jakaria, Tahmina Abeda, Nurul Absar, Raju Dash. Comput Biol Chem 2018
7
28

ABC Transporters and the Alzheimer's Disease Enigma.
Andrea Wolf, Björn Bauer, Anika M S Hartz. Front Psychiatry 2012
63
18


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.