SYED IBRAHIM B Associate Professor

Profile Picture

  • Department of Bioinformatics
  • School of Life Sciences
  • ibrahim.bic@pondiuni.edu.in

Academic Activity

Academic Activity Picture1

Academic Activity Picture2

Educational Qualification (UG,PG & Higher Order)

S.No Degree Subject/Title of thesis University/Board Year of Passing
1 Ph.D., Crystallography and Biophysics University of Madras 2005
2 M.Sc., Crystallography and Biophysics University of Madras 1999
3 B.Sc., Chemistry Bharathidasan University 1994

Area of Specializaion

Cancer Causing proteins from TLR partners: Identification of inhibitors in the TLR4 signaling cascade - Impact of SNP’s on structure and function of HMGB1, TLR and TIR domains; Bacterial Surface Proteins: Identification of inhibitors and X-Ray Crystallography study for Bacterial surface proteins; MICOS complex: Membrane proteins involved in Lipid transport mechanism are the research area of my team.

Awards / Prizes Conferred

S.No Name / Title of the Award Type Name of the Agency conferred the Award Year of the Award Amount for Cash Award

Teaching Experience

S.No Designation Department/Centre Institution
1 Assistant Professor Centre for Bioinformatics Pondicherry University

Research Experience

S.No Designation Department/Centre Institution Area of Research
1 Research Scholar Dept. of Crystallography and Biophysics University of Madras Crystallography and Biophysics
2 Post Doctoral Fellow PHRI PHRI/NJMS, UMDNJ, USA Structural Biology
3 Post Doctoral Fellow Biology Department BNL, USA Structural Biology
4 Assistant Professor Centre for Bioinformatics Pondicherry University Structural Biology

Industry Experience

S.No Designation Company/Corporate Nature of Work

Contribution towards Innovation

S.No Name of the Work/Contribution Specialization Remarks

Patent Details

S.No Title Status Patent Number Year of Award Type Commercialized Status

Papers Published in UGC Approved Journals

S.No Title Name of the Authors as per the order in Paper Journal Name Volume, Issue & Page Nos. Year Impact Factor
1 Understanding Russell’s viper venom factor V activator’s substrate specificity by surface plasmon resonance and in-silico studies. Pradeep KY., Bharathi, C., and Syed Ibrahim, B. Srinivas S Plos One., 12(7), p1-22 2017 2.806
2 Molecular characterization and application of lipase from Bacillus sp. PU1 and investigation of structural changes based on pH and temperature using M . Palanichamy E, Bharathi A. C, Balraj M, Dasari A, Repally A, Syed Ibrahim B, Arul V International Journal of Biological Macromolecules 103, p47-56., 2017 3.671
3 Exploring the binding mechanism and kinetics of Piperine with snake venom secretory Phospholipase A2. Bharathi. A.C., Sistla Srinivas and Syed Ibrahim. B. J. Biomol. Struct. Dyn. p1-12 2017 2.3
4 Sequence diversity and ligand-induced structural rearrangements of viper hyaluronidase. Bharathi, A. C.; Yadav, P. K.; Syed Ibrahim, B. Molecular Biosystems., 12, 1128 – 1138, 2016 3.2
5 Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. B. Syed Ibrahim, N. Kanneganti, G.E. Rieckhof, A. Das, D.V.Laurents, J.B.Palenchar, V. Bellofatto, and David A. Wah PNAS v106, p13242-13247 2009 9.432

Papers Published in Non UGC Approved Peer Reviewed Journals

S.No Title Name of the Authors as per the order in Paper Journal Name Volume, Issue & Page Nos. Year Impact Factor
1 Computational Investigations of Indanedione and Indanone Derivatives in Drug Discovery: Indanone Derivatives Inhibits Cereblon, an E3 Ubiquitin Ligase Upendra, N., Syed Ibrahim, B., Ummul Halilunnisa, M., Mazhuvancherry, K., Abdul Ajees, A Comp Bio and Chemistry Oct, 2022 2022 3.7
2 Structural impact of pathogenic SNPs on β-tubulin using molecular dynamics study. Ummul Halilunnisa, M., and Syed Ibrahim, B J Biomol Struct Dyn Oct 2022 2022 3.4
3 The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study Santhiya, P., Christian Bharathi, A., Syed Ibrahim, B J Biomol Struct Dyn (38), 4471-4482 2019 3.4
4 In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach Samykannu G, Vijayababu P, Antonyraj CB, Perumal P, Narayanan S, Basheer Ahamed SI, Natarajan J J Comput Biol Dec 2018 2018 0.87
5 Patulin interference with ATP binding cassette transferring auto inducer _2 in Salmonella typhi and biofilm inhibition via quorum sensing. Princy Vijayababu, Gopinath, S, Christian Bharathi, A, Thomas, J, Sundara Baalaji, N, Syed Ibrahim, B, Shanmughavel, P Informatics in Medicine Unlocked 11, p9–14. 2018 2.525
6 Cloning, over expression, purification of bacteriocin enterocin-B and structural analysis, interaction determination of enterocin-A, B against pathoge Dasari A, Esakkiraj P, Christian Bharathi A, Ayyanna R, Venkatesh P, Syed Ibrahim B, Venkatesan Arul. International Journal of Biological Macromolecules 116, p502–512 2018 3.671
7 B-cell and T-cell epitope identification with stability analysis of AI-2 import ATP-binding cassette LsrA from S. typhi eIn silico approach Princy Vijayababu, Gopinath Samykannu, Christian Bharathi Antonyraj, SundaraBaalaji Narayanan, Syed Ibrahim Basheer Ahamed, Perumal Perumal, Shanmughavel Piramanayagam Microbial Pathogenesis 123, 487–495 2018 3.7
8 Functions and Therapeutic Applications of Venom Proteins Christian Bharathi, B. Syed Ibrahim Science and Technological Research Journal V1, No1, p40-52, 2017 2017 0.1
9 Exploring the binding mechanism and kinetics of Piperine with snake venom secretory Phospholipase A2. Bharathi. A.C., Sistla Srinivas and Syed Ibrahim. B. J. Biomol. Struct. Dyn. p1-12 2017 2.3
10 Molecular characterization and application of lipase from Bacillus sp. PU1 and investigation of structural changes based on pH and temperature using M Palanichamy E, Bharathi A. C, Balraj M, Dasari A, Repally A, Syed Ibrahim B, Arul V International Journal of Biological Macromolecules 103, p47-56., 2017 3.671
11 Understanding Russell’s viper venom factor V activator’s substrate specificity by surface plasmon resonance and in-silico studies. Pradeep KY., Bharathi, C., and Syed Ibrahim, B. Srinivas S Plos One., 12(7), p1-22 2017 2.806
12 Investigations of binding mode insight in Salmonella typhi type-III secretion system tip protein (SipD): A molecular docking and MD simulation study. Gopinath S, Princy Vijayababu, Christian Bharathi A, Sundara Baalaji N, Syed Ibrahim B Informatics in Medicine Unlocked 9, p166–172 2017 2.525
13 நஞ்சு புரதங்களின் செயல்தன்மைகளும் அதன் மருத்துவ பயன்ப கிறிஸ்டியன் பாரதி, அ, சையது இப்ராஹிம், ப அறிவியல் மற்றும் தொழில்நுட்ப ஆராய்ச்சி சஞ்சிகை V1, No1, p69-90, 2017 2017 0.1
14 Sequence diversity and ligand-induced structural rearrangements of viper hyaluronidase. Bharathi, A. C.; Yadav, P. K.; Syed Ibrahim, B Molecular Biosystems., 12, 1128 – 1138, 2016 3.2
15 Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. B. Syed Ibrahim, N. Kanneganti, G.E. Rieckhof, A. Das, D.V.Laurents, J.B.Palenchar, V. Bellofatto, and David A. Wah PNAS v106, p13242-13247 2009 9.432
16 Trypsin inhibition by a peptide hormone: Crystal structure of trypsin-vasopressin complex. B. Syed Ibrahim and Vasantha Pattabhi J. Mol. Biol., 348, p1191-1198. 2005 3.871
17 Role of weak interactions in thermal stability of proteins. B. Syed Ibrahim and Vasantha Pattabhi Biochem. Biophys. Res Commun. 325, p1082-1089 2004 2.548
18 Trypsin Activity reduced by an Autocatalytically produced nonapeptide B. Syed Ibrahim, N. Shamaladevi and Vasantha Pattabhi. J. Biomol. Struct. Dyn 21, p0737 - 744. 2004 2.3
19 Crystal structure of trypsin-turkey egg white inhibitor complex. B. Syed Ibrahim and Vasantha Pattabhi Biochem. Biophys. Res Commun. 313, p8 -16 2003 2.548
20 Anti - 2, 19 - Diethoxylcarbonyl - 2, 19 - diformylamino [3.2.3.2] paracyclophane. L. Damodharan, B. Syed Ibrahim, Vasantha Pattabhi, Somnath Halder and Sambasivarao Kotha. Acta Cryst. E E58, p038 - 1039 2002 0.411

Papers Published in Conference Proceedings

S.No Title Name of the Authors as per the order in Paper Details of Conference Publication Page Nos. Year

Books

S.No Title of the Book Name of the Authors as per the order in Book Publisher Year ISBN No.

Chapters in Books

S.No Title of the Chapters Name of the Authors Title of the Book Publisher Year ISBN No.

Edited Books

S.No Title of the Book Name of the Authors as per the order in Book Publisher Year ISBN No.

Ongoing Projects

S.No Title of the Project Sponsored By Period Sanctioned Amount(Rs. Lakh) Year

Ongoing Consultancy Works

S.No Title of the Consultancy Work Sponsored By Period Sanctioned Amount(Rs. Lakh) Year

Completed Projects

S.No Title of the Project Sponsored By Period Sanctioned Amount(Rs. Lakh) Year
1 Structural and Biochemical characterization of Factor V activating enzyme (FVA) from snake venom towards drug designing and Purification, crystallisation of L-amino acid oxidase (LAAO) DST - SERB 3 Year 18.78 2012
2 Structure and Biochemical characterization of Factor V activating enzyme (FVA) from snake venom towards drug designing Pondicherry University 1 year 3 2011

Completed Consultancy Works

S.No Title of the Consultancy Work Sponsored By Period Sanctioned Amount(Rs. Lakh) Year

Career Guidance Offered to students

S.No Name of the Scheme No. of Students Competitive Examinations/ Career Counseling No. of Students Passed No. of Students Placed

List of capability enhancement such as Soft skill development, Remedial coaching, Language lab,
Bridge courses, Yoga, Meditation, Personal Counselling and Mentoring etc.,

S.No Name of the Programme/Scheme Date of Implementation No. of Students Enrolled Agencies Involved

Research Guidance - PG

S.No Year Degree No. of Students Awarded Department/Centre
1 2018 M.SC 3 Centre for Bioinformatics
2 2018 M.TECH 1 Centre for Bioinformatics
3 2017 M.SC 2 Centre for Bioinformatics
4 2017 M.TECH 1 Centre for Bioinformatics
5 2016 M.TECH 1 Centre for Bioinformatics
6 2016 M.SC 2 Centre for Bioinformatics
7 2015 M.SC 4 Centre for Bioinformatics
8 2014 M.SC 2 Centre for Bioinformatics
9 2013 M.SC 4 Centre for Bioinformatics
10 2012 M.SC 4 Centre for Bioinformatics
11 2011 M.SC 4 Centre for Bioinformatics

Research Guidance - Ph.D

S.No Student Name Registration Date Registration No. Thesis Title Thesis Submitted Status Thesis Submitted Date Vivavoce Completed Status Date Awarded
1 Pradeep Kumar Yadav 13-08-2011 R27096 Effect of structural plasticity of proteins and analysis of Ligand Binding cavity by statistical approach YES 26-10-2017 NO
2 Christian Barathi 03-07-2012 R34503 Structural and functional studies on biologically and medicinally important venom proteins YES 23-06-2017 NO
3 Thippana Mallikarjuna 18-09-2013 Study on medicinally important proteins NO NO
4 M. Karunakaran 15-06-2016 Structure and functional study of membrane proteins from bovine liver NO NO
5 Alok Kumar Pandey 01-09-2016 Structure and functional study of proteins in cancer NO NO
6 Priya Singh 01-09-2016 Study on proteins of heavy metal detoxification NO NO

Research Guidance - Post Doctoral

S.No Scholar Name Designation Funding Agency Fellowship Title Year of Joining Year of Completion

Financial assistance availed to attend conferences / workshops and to pay membership fee
of professional bodies during the year

S.No Conference/ workshop attended for which financial support provided Professional body for which membership fee is provided Amount of Support Place From Date To Date Year

E-Lecture Details

S.No E-Lecture Title Development of e-content/e-learning/delivering Member of Editorial Bodies Reviewer/Referee of
Content/Module Title Institution/Platform Year Weblink

Details of Online Education Conducted

S.No Nature of Online Course No. of Sessions Target Group Date

Invited Talks in Conference/Seminar/Workshop/Training Programme

S.No Title of the Paper Conferences/Seminar/Workshop/Training Programme Organized by Whether International / National / State / Regional / College or University Level From To Year
1 Understanding Russell’s viper venom factor V activator’s substrate specificity by surface plasmo Cross-talk in Omics Centre for Bioinformatics, Pondicherry University National 09-08-2017 09-08-2017 2017
2 Bioinformatics and Computational Biology Workshop DLS, Central University of Tamilnadu, Thiruvarur University 12-04-2016 13-04-2016 2016
3 Protein Structure in Drug Binding studies Inter Disciplinary National Seminar on Drug Design Shrimathi Devkunvar Nanalal Bhatt Vaishnav College For Women National 04-02-2015 05-02-2015 2015
4 Protein Crystallography DBT Sponsored Short-Term Training Course on “Fermentation & Bioseparation Methods” Department of Microbiology, Pondicherry University National Course 02-01-2015 17-01-2015 2015
5 Drug Binding study using Protein structures Recent trends and future advances in Life Sciences (RTFALS) Department of Life Sciences, Central University of Thiruvarur National 26-02-2015 27-02-2015 2015
6 “Biophysics - a modern tool for analysing protein structures “ Special Lecture Physics Association of Jamal Mohamed College, Trichy College 08-03-2013 08-03-2013 2013
7 “Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei One day symposium “Recent Trends in Biophysics”, Centre for Atomic and Molecular Physics, Manipal University National 25-02-2013 25-02-2013 2013
8 Crystal structure of trypanosome Transcription factor IIB” and “Crystal Structure of 2,3 dihydr Recent Trends in Structural Bioinformatics and Computer Aided Drug Design Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India National 19-02-2013 22-02-2013 2013
9 Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei 41st National Seminar on Crystallography CAS in Crystallography and Biophysics, University of Madras National 08-10-2012 10-10-2012 2012

Conferences/Seminars Organized

S.No Title of the Programme Sponsors Venue & Duration Whether International / National / State / Regional / College or University Level From To Year
1 Next Genomic Era-NGS: A Clinical Approach DBT, New Delhi and Pondicherry University Centre for Bioinformatics. Pondicherry University, 2 Day National 15-03-2018 16-03-2018 2018
2 Current Trends in Protein Structures and Genome Analysis DBT, New Delhi and Pondicherry University Centre for Bioinformatics. Pondicherry University, 1 Day University 24-02-2017 24-02-2017 2017

Workshop Organized

S.No Title of the Programme Sponsors Venue & Duration Whether International / National / State / Regional / College or University Level From To Year
1 Next Genomic Era-NGS: A Clinical Approach DBT, New Delhi, Pondicherry University Centre for Bioinformatics, Pondicherry University, 2 Days National 15-03-2018 16-03-2018 2018

Administrative Responsibilities in the Government and Quasi Government Agencies

S.No Name of the Position Agency/Organisation Duration Nature of Duties

Affiliation in Academic Bodies/Societies

S.No Name of the Body/Society Nature of Affiliation Year

Participation & Extension Activities (Academic/Administraion)

S.No Name of the Position (Head, Dean, Co-ordinator, Director, etc.,) Duration Nature of Dutites

Participation & Extension Activities (Co-Curricular)

S.No Name of the Position (NSS, NCC, Warden etc.,) Duration Nature of Dutites

Collaboration with Institution/Industry

S.No Collaborator Name Designation Institution/Industry Type Nature of Collaboration Period of Collaboration Visits to Collaborating
Institution / Industry		 Details of Collaborative Research/Teaching
From Date To Date From Date To Date

Faculty Development Programme Attended (Orientation, Refresher, other Short Term Course during the year)

S.No Title of the FDP Organiser Venue Duration From Date To Date Year

Details of Executive Development Prog/Management Development Prog. conducted

S.No Name of the Programme No. of Participants Venue Duration From Date To Date Year Revenue Generated

Participation in IMPESS, IMPRINT, SPARC, STARS, LEAP Programme etc and DSF Funding Programme

S.No IMPRESS/IMPRINT/SPARC/STARS/LEAP/Others Place From Date To Date Year

Enrolment under ARPIT Programme

S.No Name of the Programme Period of the Programme
From Date To Date