A citation-based method for searching scientific literature

Ashraya Ravikumar, Chandrasekharan Ramakrishnan, Narayanaswamy Srinivasan. Structure 2019
Times Cited: 7







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



Times Cited
  Times     Co-cited
Similarity


Stereochemistry of polypeptide chain configurations.
G N RAMACHANDRAN, C RAMAKRISHNAN, V SASISEKHARAN. J Mol Biol 1963
57

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
42


Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility.
Ashraya Ravikumar, Alexandre G de Brevern, Narayanaswamy Srinivasan. J Phys Chem B 2021
4
75

Investigations of Ramachandran disallowed conformations in protein domain families.
B Lakshmi, C Ramakrishnan, G Archunan, R Sowdhamini, N Srinivasan. Int J Biol Macromol 2014
11
28

Dynamic personalities of proteins.
Katherine Henzler-Wildman, Dorothee Kern. Nature 2007
28

Protein flexibility and rigidity predicted from sequence.
Avner Schlessinger, Burkhard Rost. Proteins 2005
120
28

CD-HIT Suite: a web server for clustering and comparing biological sequences.
Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li. Bioinformatics 2010
28

A Src-like inactive conformation in the abl tyrosine kinase domain.
Nicholas M Levinson, Olga Kuchment, Kui Shen, Matthew A Young, Michael Koldobskiy, Martin Karplus, Philip A Cole, John Kuriyan. PLoS Biol 2006
243
28

Identification of a hidden strain switch provides clues to an ancient structural mechanism in protein kinases.
Krishnadev Oruganty, Nakul Suhas Talathi, Zachary A Wood, Natarajan Kannan. Proc Natl Acad Sci U S A 2013
30
28

Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
28


Structural compromise of disallowed conformations in peptide and protein structures.
C Ramakrishnan, B Lakshmi, A Kurien, D Devipriya, N Srinivasan. Protein Pept Lett 2007
11
28

On residues in the disallowed region of the Ramachandran map.
Debnath Pal, Pinak Chakrabarti. Biopolymers 2002
53
28

The pleated sheet, a new layer configuration of polypeptide chains.
L PAULING, R B COREY. Proc Natl Acad Sci U S A 1951
352
28


A revised set of potentials for beta-turn formation in proteins.
E G Hutchinson, J M Thornton. Protein Sci 1994
740
28

PIC: Protein Interactions Calculator.
K G Tina, R Bhadra, N Srinivasan. Nucleic Acids Res 2007
638
28

Knowledge-based protein modeling.
M S Johnson, N Srinivasan, R Sowdhamini, T L Blundell. Crit Rev Biochem Mol Biol 1994
163
28

Hypervariability of accessible and inaccessible conformational space of proteins.
Ashraya Ravikumar, Narayanaswamy Srinivasan. Curr Res Struct Biol 2021
2
100

Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues.
Himani Tandon, Arun Sharma, Saruchi Wadhwa, Raghavan Varadarajan, Ramandeep Singh, Narayanaswamy Srinivasan, Sankaran Sandhya. J Biol Chem 2019
15
28

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.
Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S Raghavender, Bernardo Ochoa-Montaño, Alicia P Higueruelo, Ramanathan Sowdhamini, Nagasuma R Chandra, Tom L Blundell,[...]. Database (Oxford) 2015
7
28

Reliability of atomic displacement parameters in protein crystal structures.
O Carugo, P Argos. Acta Crystallogr D Biol Crystallogr 1999
28
14

PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations.
Gerard Martínez-Rosell, Toni Giorgino, Gianni De Fabritiis. J Chem Inf Model 2017
79
14


The origin of allosteric functional modulation: multiple pre-existing pathways.
Antonio del Sol, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov. Structure 2009
283
14


Aurora A, meiosis and mitosis.
Richard Crane, Bedrick Gadea, Laurie Littlepage, Hua Wu, Joan V Ruderman. Biol Cell 2004
120
14


Conformation of polypeptides and proteins.
G N Ramachandran, V Sasisekharan. Adv Protein Chem 1968
14

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
14



A helix scaffold for the assembly of active protein kinases.
Alexandr P Kornev, Susan S Taylor, Lynn F Ten Eyck. Proc Natl Acad Sci U S A 2008
296
14


Localizing frustration in native proteins and protein assemblies.
Diego U Ferreiro, Joseph A Hegler, Elizabeth A Komives, Peter G Wolynes. Proc Natl Acad Sci U S A 2007
222
14


Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
14

ACPYPE - AnteChamber PYthon Parser interfacE.
Alan W Sousa da Silva, Wim F Vranken. BMC Res Notes 2012
14


Allostery: absence of a change in shape does not imply that allostery is not at play.
Chung-Jung Tsai, Antonio del Sol, Ruth Nussinov. J Mol Biol 2008
345
14

Disallowed Ramachandran conformations of amino acid residues in protein structures.
K Gunasekaran, C Ramakrishnan, P Balaram. J Mol Biol 1996
78
14

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.
Li-Quan Yang, Peng Sang, Yan Tao, Yun-Xin Fu, Ke-Qin Zhang, Yue-Hui Xie, Shu-Qun Liu. J Biomol Struct Dyn 2014
66
14



Local dynamics of proteins and DNA evaluated from crystallographic B factors.
Bohdan Schneider, Jean Christophe Gelly, Alexandre G de Brevern, Jiří Černý. Acta Crystallogr D Biol Crystallogr 2014
35
14

Objectively judging the quality of a protein structure from a Ramachandran plot.
R W Hooft, C Sander, G Vriend. Comput Appl Biosci 1997
169
14

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
R A Laskowski, J A Rullmannn, M W MacArthur, R Kaptein, J M Thornton. J Biomol NMR 1996
14

On the relation between residue flexibility and local solvent accessibility in proteins.
Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz Kurgan. Proteins 2009
65
14



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.