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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

Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions

Malhotra, S., Sowdhamini, R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.60 MB

english, 2013

7

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

8

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

9

SMotif: a server for structural motifs in proteins

Pugalenthi, G., Suganthan, P. N., Sowdhamini, R., Chakrabarti, S.

Journal:

Year:

2007

Language:

english

File:

PDF, 72 KB

english, 2007

10

SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs

Chakrabarti, S., Anand, A. P., Bhardwaj, N., Pugalenthi, G., Sowdhamini, R.

Journal:

Nucleic Acids Research

Year:

2005

Language:

english

File:

PDF, 55 KB

english, 2005

11

Variation in Antibiotic Selection and Clinical Outcomes in Infants

Markham, Jessica L., Hall, Matthew, Queen, Mary Ann, Aronson, Paul L., Wallace, Sowdhamini S., Foradori, Dana M., Hester, Gabrielle, Nead, Jennifer, Lopez, Michelle A., Cruz, Andrea T., McCulloh, Russ

Journal:

Hospital Pediatrics

Year:

2019

Language:

english

File:

PDF, 1.06 MB

english, 2019

12

Caregivers’ Perceptions and Hospital Experience After a Brief Resolved Unexplained Event: A Qualitative Study

Khan, Adrita, Wallace, Sowdhamini S., Sampayo, Esther M., Falco, Carla

Journal:

Hospital Pediatrics

Year:

2019

Language:

english

File:

PDF, 728 KB

english, 2019

13

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

14

The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor

Rupali A. Gadkari, S. Sandhya, R. Sowdhamini, Rajan R. Dighe

Journal:

Molecular and Cellular Endocrinology

Year:

2007

Language:

english

File:

PDF, 781 KB

english, 2007

15

[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

16

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

17

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

18

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

R. Sowdhamini, Tom L. Blundell

Journal:

Protein Science

Year:

1995

Language:

english

File:

PDF, 8.74 MB

english, 1995

19

Domain architectural census of eukaryotic gene products containing O-protein phosphatases

Anirban Bhaduri, R. Sowdhamini

Journal:

Year:

2006

Language:

english

File:

PDF, 689 KB

english, 2006

20

Prediction of Functional Sites in Proteins Using Conserved Functional Group Analysis

C.Axel Innis, A.Prem Anand, R. Sowdhamini

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.33 MB

english, 2004

21

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

22

A genome-wide survey of human tyrosine phosphatases

Bhaduri, A., Sowdhamini, R.

Journal:

Protein Engineering Design and Selection

Year:

2003

Language:

english

File:

PDF, 328 KB

english, 2003

23

SMoS: a database of structural motifs of protein superfamilies

Chakrabarti, S., Venkatramanan, K., Sowdhamini, R.

Journal:

Protein Engineering Design and Selection

Year:

2003

Language:

english

File:

PDF, 144 KB

english, 2003

24

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

25

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

26

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

27

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Ratna R Thangudu, Malini Manoharan, N Srinivasan, Frédéric Cadet, R Sowdhamini, Bernard Offmann

Journal:

BMC Structural Biology

Year:

2008

Language:

english

File:

PDF, 4.19 MB

english, 2008

28

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

29

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

30

[IEEE 2011 IEEE International Conference on Data Mining Workshops (ICDMW) - Vancouver, BC, Canada (2011.12.11-2011.12.11)] 2011 IEEE 11th International Conference on Data Mining Workshops - Mining Protein Sequence Databases for Remote Homologues That Can Display Considerable Domain Length Variations

Mutt, Eshita, Mitra, Abhijit, Sowdhamini, R.

Year:

2011

Language:

english

File:

PDF, 419 KB

english, 2011

31

LenVarDB: database of length-variant protein domains

Mutt, E., Mathew, O. K., Sowdhamini, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.21 MB

english, 2014

32

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

33

iMOT: an interactive package for the selection of spatially interacting motifs

Bhaduri, A., Pugalenthi, G., Gupta, N., Sowdhamini, R.

Journal:

Nucleic Acids Research

Year:

2004

Language:

english

File:

PDF, 291 KB

english, 2004

34

A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities

Ghosh, Pritha, Grellscheid, Sushma Nagaraja, Sowdhamini, R.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 1.30 MB

english, 2015

35

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

36

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

37

The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL

Neha Parikh, Caroline Koshy, Vaigundan Dhayabaran, Lakshmi R Perumalsamy, R Sowdhamini, Apurva Sarin

Journal:

BMC Cell Biology

Year:

2007

Language:

english

File:

PDF, 2.37 MB

english, 2007

38

Foreword

N Srinivasan, R Sowdhamini, Alok Bhattacharya

Journal:

Journal of Biosciences

Year:

2007

Language:

english

File:

PDF, 170 KB

english, 2007

39

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

40

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

41

Localization of Functional Domains of the Mitogenic Toxin of Pasteurella multocida

Pullinger, G. D., Sowdhamini, R., Lax, A. J.

Journal:

Infection and Immunity

Year:

2001

Language:

english

File:

PDF, 1.76 MB

english, 2001

42

Molecular Mechanisms of Cardiomyopathy-Causing TnT Mutants Implicated in Interactions with Tropomyosin

Gangadharan, Binnu, Mukherjee, Souhrid, Sunitha, Margaret S., Dubey, Ashvini, Sowdhamini, R., Spudich, James A., Mercer, John A.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 45 KB

english, 2016

43

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

44

The Recognition of Protein Structure and Function from Sequence: Adding Value to Genome Data [and Discussion]

May, A. C. W., Johnson, M. S., Rufino, S. D., Wako, H., Zhu, Z.-Y., Sowdhamini, R., Srinivasan, N., Rodionov, M. A., Blundell, T. L., Dover, G. A.

Journal:

Philosophical Transactions Biological Sciences

Year:

1994

Language:

english

File:

PDF, 2.00 MB

english, 1994

45

Evolutionary traces decode molecular mechanism behind fast pace of myosin XI

Divya P Syamaladevi, R Sowdhamini

Journal:

BMC Structural Biology

Year:

2011

Language:

english

File:

PDF, 1.11 MB

english, 2011

46

Genome-wide Survey of Prokaryotic O-protein Phosphatases

Anirban Bhaduri, R. Sowdhamini

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 1.17 MB

english, 2005

47

Insights into the structure of hepatocyte growth factor/scatter factor (HGF/SF) and implications for receptor activation

Dimitri Y Chirgadze, Jonathan Hepple, R.Andrew Byrd, R Sowdhamini, Tom L Blundell, Ermanno Gherardi

Journal:

Year:

1998

Language:

english

File:

PDF, 253 KB

english, 1998

48

Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. melanogaster

Sowdhamini,, K. Harini,, Sowdhamini,

Journal:

Bioinformatics and Biology Insights

Year:

2012

Language:

english

File:

PDF, 6.31 MB

english, 2012

49

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

50

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

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