Ramanathan, Sowdhamini: search on Z-Library

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1

GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies

Iyer, Meenakshi S, Bhargava, Kartik, Pavalam, Murugavel, Sowdhamini, Ramanathan

Journal:

Year:

2019

Language:

english

File:

PDF, 15.39 MB

english, 2019

2

A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure

Batra, Srishti, Corcoran, Jacob, Zhang, Dan-Dan, Pal, Pramit, K.P., Umesh, Kulkarni, Renuka, Löfstedt, Christer, Sowdhamini, Ramanathan, Olsson, Shannon B.

Journal:

Frontiers in Cellular Neuroscience

Year:

2019

Language:

english

File:

PDF, 6.87 MB

english, 2019

3

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

Sharma, Abhishek, Tiwari, Vikas, Sowdhamini, Ramanathan

Journal:

Journal of Biosciences

Year:

2020

File:

PDF, 1.88 MB

2020

4

Proteome profile of a pandemic Vibrio parahaemolyticus SC192 strain in the planktonic and biofilm condition

Dharmaprakash, Akhilandeswarre, Mutt, Eshita, Jaleel, Abdul, Ramanathan, Sowdhamini, Thomas, Sabu

Journal:

Year:

2014

Language:

english

File:

PDF, 1.03 MB

english, 2014

5

Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding

Kanagarajadurai, Karuppiah, Malini, Manoharan, Bhattacharya, Aditi, Panicker, Mitradas M., Sowdhamini, Ramanathan

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.51 MB

english, 2009

6

An in-silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway

Mahita, Jarjapu, Harini, K., Pichika, Mallikarjuna Rao, Sowdhamini, Ramanathan

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 3.15 MB

english, 2015

7

Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints

Saikat Chakrabarti, Jaisurya John, Ramanathan Sowdhamini

Journal:

Journal of Molecular Modeling

Year:

2004

Language:

english

File:

PDF, 427 KB

english, 2004

8

Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family

Naveenkumar, Nagarajan, Sowdhamini, Ramanathan, Srinivasan, Narayanaswamy

Journal:

Year:

2019

Language:

english

File:

PDF, 1.44 MB

english, 2019

9

[IEEE 2010 IEEE International Conference on Data Mining Workshops (ICDMW) - Sydney, TBD, Australia (2010.12.13-2010.12.13)] 2010 IEEE International Conference on Data Mining Workshops - A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families

Gowri, V.S., Shameer, Khader, Reddy, Chilamakuri Chandra Sekhar, Shingate, Prashant, Sowdhamini, Ramanathan

Year:

2010

Language:

english

File:

PDF, 504 KB

english, 2010

10

Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space

Kaushik, Swati, Nair, Anu G, Mutt, Eshita, Subramanian, Hari Prasanna, Sowdhamini, Ramanathan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

11

Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions

Malhotra, Sony, Sankar, Kannan, Sowdhamini, Ramanathan, Uversky, Vladimir N.

Journal:

Year:

2014

Language:

english

File:

PDF, 961 KB

english, 2014

12

Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Margaret S Sunitha, Anu G Nair, Amol Charya, Kamalakar Jadhav, Sami Mukhopadhyay, Ramanathan Sowdhamini

Journal:

BMC Research Notes

Year:

2012

Language:

english

File:

PDF, 780 KB

english, 2012

13

DOCKSCORE: a webserver for ranking protein-protein docked poses

Malhotra, Sony, Mathew, Oommen K, Sowdhamini, Ramanathan

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.52 MB

english, 2015

14

Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses

Barah, Pankaj, B N, Mahantesha Naika, Jayavelu, Naresh Doni, Sowdhamini, Ramanathan, Shameer, Khader, Bones, Atle M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.70 MB

english, 2015

15

GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies

Iyer, Meenakshi S, Bhargava, Kartik, Pavalam, Murugavel, Sowdhamini, Ramanathan

Journal:

Year:

2019

File:

PDF, 15.39 MB

2019

16

Fold prediction and comparative modeling of Bdm1: a probable α/β hydrolase associated with hot water epilepsy

Anirban Bhaduri, Lakshminarasimhan Krishnaswamy, Gautam R. Ullal, Mitradas M. Panicker, Ramanathan Sowdhamini

Journal:

Journal of Molecular Modeling

Year:

2003

Language:

english

File:

PDF, 393 KB

english, 2003

17

Improvement of alignment accuracy utilizing sequentially conserved motifs

Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.34 MB

english, 2004

18

172 Computational analysis and prediction of proteins that undergo domain swapping

Shingate, Prashant, Upadhyay, Atul, Khader, Shameer, Sowdhamini, Ramanathan

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 572 KB

english, 2015

19

Investigating the effect of key mutations on the conformational dynamics of Toll-like receptor dimers through molecular dynamics simulations and protein structure networks

Mahita, Jarjapu, Sowdhamini, Ramanathan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 2.44 MB

english, 2018

20

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Ghosh, Pritha, Mathew, Oommen K., Sowdhamini, Ramanathan

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 2.58 MB

english, 2016

21

Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome

Khader Shameer, Ramanathan Sowdhamini

Journal:

Journal of Clinical Bioinformatics

Year:

2012

Language:

english

File:

PDF, 820 KB

english, 2012

22

Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

Mudgal, Richa, Sowdhamini, Ramanathan, Chandra, Nagasuma, Srinivasan, Narayanaswamy, Sandhya, Sankaran

Journal:

Journal of Molecular Biology

Year:

2014

Language:

english

File:

PDF, 1.11 MB

english, 2014

23

Modeling and Conformational Analysis of Cyclotides, a Class of Macrocyclic Disulfide Bonded Plant Peptides

Kalmankar, Neha V., Balaram, P., Ramanathan, Sowdhamini, Venkatesan, Radhika

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 50 KB

english, 2018

24

Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening

Harini, K., Sowdhamini, Ramanathan, Matsunami, Hiroaki

Journal:

Year:

2015

Language:

english

File:

PDF, 5.27 MB

english, 2015

25

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies

Sukhwal, Anshul, Sowdhamini, Ramanathan

Journal:

Molecular BioSystems

Year:

2013

Language:

english

File:

PDF, 3.31 MB

english, 2013

26

Specificity and stability of transient protein–protein interactions

Vishwanath, Sneha, Sukhwal, Anshul, Sowdhamini, Ramanathan, Srinivasan, Narayanaswamy

Journal:

Current Opinion in Structural Biology

Year:

2017

Language:

english

File:

PDF, 1.43 MB

english, 2017

27

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

Ogasawara, Takeshi, Cheng, Yinhe, Tzeng, Tzy-Hwa Kathy, Sowdhamini, Ramanathan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.39 MB

english, 2016

28

100 ns Molecular Dynamics Simulations to Study Intramolecular Conformational Changes in Bax

Koshy, Caroline, Parthiban, Marimuthu, Sowdhamini, Ramanathan

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2010

Language:

english

File:

PDF, 2.98 MB

english, 2010

29

Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations

Kaushik, Swati, Etchebest, Catherine, Sowdhamini, Ramanathan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

30

Sequence search and analysis of gene products containing RNA recognition motifs in the human genome

Sony Malhotra,Ramanathan Sowdhamini

Journal:

Year:

2014

Language:

english

File:

PDF, 1.03 MB

english, 2014

31

Collation and analyses of DNA-binding protein domain families from sequence and structural databanks

Malhotra, Sony, Sowdhamini, Ramanathan

Journal:

Molecular BioSystems

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

32

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Shameer, Khader, Tripathi, Lokesh P., Kalari, Krishna R., Dudley, Joel T., Sowdhamini, Ramanathan

Journal:

Briefings in Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

33

Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region

Gangadharan, Binnu, Sunitha, Margaret S., Mukherjee, Souhrid, Chowdhury, Ritu Roy, Haque, Farah, Sekar, Narendrakumar, Sowdhamini, Ramanathan, Spudich, James A., Mercer, John A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1003 KB

english, 2017

34

Genome inventory and analysis of nuclear hormone receptors inTetraodon nigroviridis

Raghu Prasad Rao Metpally, Ramakrishnan Vigneshwar, Ramanathan Sowdhamini

Journal:

Journal of Biosciences

Year:

2007

Language:

english

File:

PDF, 324 KB

english, 2007

35

Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3

Mahita, Jarjapu, Sowdhamini, Ramanathan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

36

Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Kaushik, Swati, Mutt, Eshita, Chellappan, Ajithavalli, Sankaran, Sandhya, Srinivasan, Narayanaswamy, Sowdhamini, Ramanathan, Promponas, Vasilis J.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

37

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Khader Shameer, Lalima L Madan, Shivamurthy Veeranna, Balasubramanian Gopal, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 884 KB

english, 2010

38

Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics

Naika, Mahantesha, Shameer, Khader, Sowdhamini, Ramanathan

Journal:

Molecular BioSystems

Year:

2013

Language:

english

File:

PDF, 23.94 MB

english, 2013

39

Knowledge-Based Protein Modeling

Johnson, Mark S., Srinivasan, Narayanaswamy, Sowdhamini, Ramanathan, Blundell, Tom L

Journal:

Critical Reviews in Biochemistry and Molecular Biology

Year:

1994

Language:

english

File:

PDF, 5.27 MB

english, 1994

40

Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions

Ramanathan, Sowdhamini, Malini, Manoharan, Sankar, Kannan, Bernard, Offmann, Ramanathan, Sowdhamini

Journal:

Bioinformatics and Biology Insights

Year:

2013

Language:

english

File:

PDF, 7.40 MB

english, 2013

41

Sequence Analysis and Evolutionary Studies of Reelin Proteins

Manoharan, Malini, Muhammad, Sayyed Auwn, Sowdhamini, Ramanathan

Journal:

Bioinformatics and Biology Insights

Year:

2015

Language:

english

File:

PDF, 2.06 MB

english, 2015

42

PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena

Harbi, Djamel, Parthiban, Marimuthu, Gendoo, Deena M. A., Ehsani, Sepehr, Kumar, Manish, Schmitt-Ulms, Gerold, Sowdhamini, Ramanathan, Harrison, Paul M., Mouillet-Richard, Sophie

Journal:

Year:

2012

Language:

english

File:

PDF, 573 KB

english, 2012

43

Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins

Shingate, Prashant, Warwicker, Jim, Sowdhamini, Ramanathan, Permyakov, Eugene A.

Journal:

Year:

2015

Language:

english

File:

PDF, 5.59 MB

english, 2015

44

Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes

Iyer, Meenakshi S., Joshi, Adwait G., Sowdhamini, Ramanathan

Journal:

Molecular Omics

Year:

2018

Language:

english

File:

PDF, 1.26 MB

english, 2018

45

PURE: A webserver for the prediction of domains in unassigned regions in proteins

Chilamakuri CS Reddy, Khader Shameer, Bernard O Offmann, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

46

POEAS: Automated Plant Phenomic Analysis Using Plant Ontology

Shameer, Khader, Naika, Mahantesha Bn, Mathew, Oommen K., Sowdhamini, Ramanathan

Journal:

Bioinformatics and Biology Insights

Year:

2014

Language:

english

File:

PDF, 2.05 MB

english, 2014

47

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

Xue, Zhidong, Jang, Richard, Govindarajoo, Brandon, Huang, Yichu, Wang, Yan, Sowdhamini, Ramanathan

Journal:

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

48

Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach

Shameer, Khader, Pugalenthi, Ganesan, Kandaswamy, Krishna Kumar, Suganthan, Ponnuthurai N., Archunan, Govindaraju, Sowdhamini, Ramanathan

Journal:

Bioinformatics and Biology Insights

Year:

2010

Language:

english

File:

PDF, 926 KB

english, 2010

49

PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots

Sukhwal, Anshul, Sowdhamini, Ramanathan

Journal:

Bioinformatics and Biology Insights

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

50

Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures

Bhattacharyya, Teerna, Sowdhamini, Ramanathan

Journal:

Evolutionary Bioinformatics

Year:

2019

Language:

english

File:

PDF, 981 KB

english, 2019

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