Today we are ruled by chemical reactions with in ourself and around us. I started this blog to share the chemical knowledge gained over past twenty five years (1986-2013). The topics need not be connected well and each blog would certainly help to refresh the chemical science.
Why did I take chemistry as a career?
I took chemistry as the specialization as Bachelor level (Tagore Arts College, Pondicherry, Pondicherry University) after my schooling (Jeevanandam Government Higher Secondary School) mainly due to my private teacher Mr Vishwakumar, during 1985-86.
It was a tough situation moving from native language to English medium school. I joined Mr Vishwakumar who was Gold Medalist in MPhil for private tuition for mathematics, physics and chemistry (MPC). The first few days were totally 'blank', honestly as I could not the meaning for a any scientific term. A week after there was a 'internal test' usually to test the 'worthiness of both learning and teaching'. Shockingly I got 3 out of 30 ! That is the day, which made me to realize, I have to work much harder than the toppers who got 30 out 30. Hardwork and Discipline finally paid, after two years when I got 30 out 30 in the internal test, definitely I could see a SMILE in the face of my teacher. Board exam results were good enough to secure a seat in Bachelor of Science (Chemistry) in Tagore Arts College. The toppers moved to Engineering or Medicals. I decided to stay with my chemistry subject.
College Chemistry
During college days at a bachelor's level, I studied Organic Chemistry, Inorganic Chemistry, Physical Chemistry, Analytical Chemistry and Environmental chemistry. One of my favorite subject was Organic chemistry mainly due to 'Picture worth 1000 words' and with little logic one can easily understand the chemical structures, reactions, reagents, mechanism etc., After completing chemistry at bachelor's level, I decided to study Master's in Chemistry to understand the subject in depth, to secure better job in a chemical industry as a chemist or a Teacher in a School or College (Inspired by my teachers).
During the Master's in Science (Chemistry) at Centre for Post-Graduate Studies, Pondicherry, we were the first batch students of Pondicherry University. It is always challenging to be 'First'. In the Master's level we studied Organic Chemistry, Physical Chemistry, Inorganic chemistry in depth along with practicals. One of my hobby is to visit public libraries (Roman Rolland Library) and take memberships to avail the benefits of reading books of International Standards in addition to recommended books by the teachers and professors.Some of my favorite books in Organic Chemistry were related to Organic Synthesis (Norman, Carruthers, March, Morrison & Boyd etc.,) Inorganic Chemisty (Cotton & Wilkinson), Physical Chemistry (Atkins). Spectroscopy by Silverstein, Kemp, Dyer etc., Polymer Chemistry by Bill meyer, Chemical Kinetics by Laidler.
PhD in Chemistry
One of the good things I learnt during my education is to take notes during the class, and write notes at home by referring several text books on the same topics. It finally helped to clear GATE'91 and CSIR-NET1991 (June) examinations. These competitive exams opened the door of opportunities in chemical research, where I got chance to appear for interviews, and selected for PhD admission in University of Madras, Indian Institute of Technology-Madras, Indian Institute of Science-Bangalore, National Chemical Laboratory etc., I used to subscribe and read Science Reporter a magazine from Council of Scientific Industrial Research which helped to select the institute of my interest that is National Chemical Laboratory after receiving invitation from several distinguished scientists from this lab. I joined my PhD program (Dec 1991) in the area of Organic Chemistry under the supervision of Dr Ganesh Pandey, a well known organic chemist, and contributed significantly in Synthetic Organic Chemistry and Photoinduced Electron Transfer Chemistry. I could learn and discover few important C-C bond formation reactions for carbo-annulation and spiro-annulation during my research career. During the PhD program, I developed interest in computer-chemistry and that helped to pursue my carrier as an Information chemist and eventually a chemoinformatician by profession.
Chemoinformatics
When two scientific disciplines meet, they can be mutually beneficial, fill each other’s voids – and complement each other, giving rise to unprecedented scientific opportunities. One such field of recent interest is chemoinformatics. Chemoinformatics plays a key role in areas as diverse as chemical genomics and drug discovery, the storage of chemical information in databases and the prediction of toxic substances. Today, these techniques are mostly used in pharmaceutical companies in the process of drug discovery, but also for example in “functional foods”, designed by nutritional companies to improve body functions, such as for example digestion or brain function.
While bioinformatics is known since 1976 which is defined as “the study of informatics process in biotic systems”, the emerging terminology in the pharmaceutical sector is commonly referred to as chemoinformatics, which is defined as the “mixing of information resources to transform data into information and information into knowledge, intending for better rapid decisions in the arena of drug lead identification and optimization”. Chemoinformatics is a generic term that encompasses the design, creation, organization, storage, management, retrieval, analysis, dissemination, visualization and the use of chemical information – so, virtually every area where “chemical data” is accessed or changed by means of computers.
Chemoinformatics represents a vital link between experiment and theory in the area of drug design, through the extraction of information from data and conversion into knowledge. With the explosion of publicly available genomic information, such as that resulting from the Human Genome Project, in the middle of the 1990s, bioinformatics has become very popular not only in the scientific community but also among the general audience. This has led to the coining of the counterpart of bioinformatics in chemistry after about two decades as Chemoinformatics. However this field can actually be seen as about two hundred years old – ever since the first account of chemical data has been published in literature. Today’s technology in chemoinformatics in fact facilitates better organization, storage, retrieval and analysis of these data for further advanced predicting studies – thus, saving time and money, also possibly animal experiments, and advancing humankind by developing novel, and safer, drugs.
The last three decades have seen tremendous growth in this field with the advancement in the computer technologies. Today volumes and volumes of books has been written on this subject and even few text books available for teaching in universities at the BSc and MSc level. Though there are full time Masters degree programs available in universities abroad, in India this field has yet to get full recognition. Currently chemoinformatics is being introduced as part of an ongoing diploma or masters program in bioinformatics in spite of its maturity as a new discipline. Besides the traditional mainstream areas of chemoinformatics such as :
Chemistry has already evolved from largely a study of the elements to a study of molecules to currently a study of molecular interactions, especially those involving biological macromolecules – the molecules such as proteins and sugars we humans are made of. This offers a excellent opportunity for chemoinformatics to grow in this new direction. The main focus of recently identified “cyber enabled chemistry” by the US National Science Foundation is on the development of integrated databases, data mining tools, molecular visualization and computational capabilities and the remote and networked use of instrumentation.
The scope of this rapidly developing field will certainly continue to expand. It is worth mentioning that there is a new trend of integration of chemoinformatics with bioinformatics. This is because many sectors of the chemical and pharmaceutical industries are interdisciplinary by nature, and major progress and developments in those industries are occurring in both bioinformatics and chemoinformatics side by side. Chemists will become more and more computer dependent, Internet dependent and chemoinformatics dependent.
Chemoinformatics through its development in the past half a century, has reached in the present wide acceptance, and will have a bright future! The purpose of this particular article is to highlight the various research and job opportunities available to a new generation of students in chemistry, computer science and biology at various levels in both academic and pharmaceutical environment.
Job Title of Recent Graduates
Graduates from the MSc in Chemoinformatics have taken up a variety of different types of posts upon starting employment. Examples of the job titles of recent graduates are given below: Chemoinformatics Scientist, Computational Chemist, Chemical Data Scientist, Regulatory Affairs Officer, Senior Information Analyst, Information Officer, Data Officer, Graduate IT Trainee, Programmer, QSAR Software Tester, Support Analyst, Business Analyst, Technical Editor, Consultant, Research Assistant Organizations/Companies of Recent Graduates etc., Graduates from the MSc in Chemoinformatics obtain posts with a wide range of organizations and companies.
Current positions in Chemoinformatics:
(Apply Now for Project Assistant : BE/BTech/MS bioinformatics, comp. Last date 16/6/11 click here)
Some of the companies sponsoring chemoinformatics products and activities include:
[Career opportunities in Chemoinformatics : Sales, Product development, use, research]
* Accelrys
* ACD/Labs (Advanced Chemistry Development, Inc.)
* Afferent Systems Inc.
* Agilent Technologies
* Aureus Pharma
* Barnard Chemical Information Ltd. (John Barnard and Geoff Downs) SEE: digital chemistry
* Bio-Rad Laboratories
* BioReason
* BioSolveIT
* BlueObelisk.org
* Bruker Daltonics Inc.
* Cambridge Crystallographic Data Centre
* CambridgeSoft Corporation
* CARB Center for Advanced Research in Biotechnology (NIST/University of Maryland)
* Cengent Therapeutics (Genes to Leads). Acquired by Inncardio, Inc.
* Center for Molecular Modeling (NIH)
* Centre for Molecular and Biomolecular Informatics CMBI
* Cerep
* ChemAxon
* ChemDiv, Inc. (Chemical Diversity)
* Chemical Abstracts Service
* Chemical Computing Group, Inc.
* Chemical Simulations Group
* ChemInnovation Software
* ChemNavigator
* ChemSW (Chemistry Software for Windows, formerly: WindowChem)
* Chenomx Inc.
* CIS Chemical Information System
* CombiChem.net
* CompuChem
* CrossFire Beilstein
* CSA Cambridge Scientific Abstracts
* Daylight Chemical Information Systems
* Derwent (Thomson)
* Dialog (Thomson)
* digital chemistry (formerly BCI, Barnard Chemical Information)
* Drug Design Methodologies
* eduSoft (Glen E. Kellogg, Donald J. Abraham) (hint!, molconn-z, HASL)
* Eidogen-Sertanty
* Elsevier MDL
* European Bioinformatics Institute (EMBL)
* FamilyGenetix (formerly, Cherwell Scientific) (Cyrillic, ModelMaker, Modelmanager)
* FIZ Chemie Berlin (Fachinformationszentrum Chemie GmbH)
* Fujitsu (CAChe)
* Gaussian
* GCC GenChemiCs (William J. (Bill) Welsh)
* gNova Scientific Software
* GridChem
* Hypercube, Inc.
* Iconix Pharmaceuticals
* IDBS
* Incyte
* InforSense (ChemSense, InforSense KDE)
* Inpharmatica Ltd. (Biopendium, Chematica)
* Invitrogen (Vector NTI)
* IOS Improved Outcomes Software (GeneLinker)
* ISI Web of Knowledge (Thomson Scientific)
* Jubilant Biosys
* Knovel
* LabVantage
* LabWare
* LeadScope, Inc.
* Lhasa Limited
* LION bioscience
* Matrix Science
* MEDIT – Molecular Extended Distribution in Information Technology
* Metaphorics, LLC
* Modgraph Consultants, Ltd.
* Molecular Connections (Netpro)
* Molecular Discovery
* Molecular Networks
* Molecular Solutions (Recruiting Company for computational chemistry and informatics)
* Molegro
* Molinspiration
* MolMine Bioinformatics Software Solutions
* Molsearch
* MolSoft (ICM)
* NCBI US National Center for Biotechnology Information
* New River Kinematics (MoluCAD)
* NLM US National Library of Medicine
* OpenEye Scientific Software
* Ovid
* Pharma Algorithms
* Princeton Simulations (Conformer)
* Proteome Systems
* Q-Chem, Inc.
* Questel/Orbit, Inc.
* Rosetta Biosoftware
* Schrödinger
* SciTegic
* Semantic Laboratories
* SemiChem (AMPAC, Codessa)
* Serena Software, Inc. (Pcmodel)
* STN
* Sunset Molecular Discovery, LLC
* Symyx Technologies
* TDS Technical Database Services, Inc. (DIPPR/EHS, COSMOtherm, LogKOW)
* TimTec
* Tripos
* Waters (Empower, NuGenesis, MassLynx)
* Wavefunction (Spartan)
* Wiley-VCH Publishers
* WinMOPAC (Fujitsu)
Chemoinformatics helped to answer some of the fundamental questions.
Why did I take chemistry as a career?
I took chemistry as the specialization as Bachelor level (Tagore Arts College, Pondicherry, Pondicherry University) after my schooling (Jeevanandam Government Higher Secondary School) mainly due to my private teacher Mr Vishwakumar, during 1985-86.
It was a tough situation moving from native language to English medium school. I joined Mr Vishwakumar who was Gold Medalist in MPhil for private tuition for mathematics, physics and chemistry (MPC). The first few days were totally 'blank', honestly as I could not the meaning for a any scientific term. A week after there was a 'internal test' usually to test the 'worthiness of both learning and teaching'. Shockingly I got 3 out of 30 ! That is the day, which made me to realize, I have to work much harder than the toppers who got 30 out 30. Hardwork and Discipline finally paid, after two years when I got 30 out 30 in the internal test, definitely I could see a SMILE in the face of my teacher. Board exam results were good enough to secure a seat in Bachelor of Science (Chemistry) in Tagore Arts College. The toppers moved to Engineering or Medicals. I decided to stay with my chemistry subject.
College Chemistry
During college days at a bachelor's level, I studied Organic Chemistry, Inorganic Chemistry, Physical Chemistry, Analytical Chemistry and Environmental chemistry. One of my favorite subject was Organic chemistry mainly due to 'Picture worth 1000 words' and with little logic one can easily understand the chemical structures, reactions, reagents, mechanism etc., After completing chemistry at bachelor's level, I decided to study Master's in Chemistry to understand the subject in depth, to secure better job in a chemical industry as a chemist or a Teacher in a School or College (Inspired by my teachers).
During the Master's in Science (Chemistry) at Centre for Post-Graduate Studies, Pondicherry, we were the first batch students of Pondicherry University. It is always challenging to be 'First'. In the Master's level we studied Organic Chemistry, Physical Chemistry, Inorganic chemistry in depth along with practicals. One of my hobby is to visit public libraries (Roman Rolland Library) and take memberships to avail the benefits of reading books of International Standards in addition to recommended books by the teachers and professors.Some of my favorite books in Organic Chemistry were related to Organic Synthesis (Norman, Carruthers, March, Morrison & Boyd etc.,) Inorganic Chemisty (Cotton & Wilkinson), Physical Chemistry (Atkins). Spectroscopy by Silverstein, Kemp, Dyer etc., Polymer Chemistry by Bill meyer, Chemical Kinetics by Laidler.
PhD in Chemistry
One of the good things I learnt during my education is to take notes during the class, and write notes at home by referring several text books on the same topics. It finally helped to clear GATE'91 and CSIR-NET1991 (June) examinations. These competitive exams opened the door of opportunities in chemical research, where I got chance to appear for interviews, and selected for PhD admission in University of Madras, Indian Institute of Technology-Madras, Indian Institute of Science-Bangalore, National Chemical Laboratory etc., I used to subscribe and read Science Reporter a magazine from Council of Scientific Industrial Research which helped to select the institute of my interest that is National Chemical Laboratory after receiving invitation from several distinguished scientists from this lab. I joined my PhD program (Dec 1991) in the area of Organic Chemistry under the supervision of Dr Ganesh Pandey, a well known organic chemist, and contributed significantly in Synthetic Organic Chemistry and Photoinduced Electron Transfer Chemistry. I could learn and discover few important C-C bond formation reactions for carbo-annulation and spiro-annulation during my research career. During the PhD program, I developed interest in computer-chemistry and that helped to pursue my carrier as an Information chemist and eventually a chemoinformatician by profession.
Chemoinformatics
When two scientific disciplines meet, they can be mutually beneficial, fill each other’s voids – and complement each other, giving rise to unprecedented scientific opportunities. One such field of recent interest is chemoinformatics. Chemoinformatics plays a key role in areas as diverse as chemical genomics and drug discovery, the storage of chemical information in databases and the prediction of toxic substances. Today, these techniques are mostly used in pharmaceutical companies in the process of drug discovery, but also for example in “functional foods”, designed by nutritional companies to improve body functions, such as for example digestion or brain function.
While bioinformatics is known since 1976 which is defined as “the study of informatics process in biotic systems”, the emerging terminology in the pharmaceutical sector is commonly referred to as chemoinformatics, which is defined as the “mixing of information resources to transform data into information and information into knowledge, intending for better rapid decisions in the arena of drug lead identification and optimization”. Chemoinformatics is a generic term that encompasses the design, creation, organization, storage, management, retrieval, analysis, dissemination, visualization and the use of chemical information – so, virtually every area where “chemical data” is accessed or changed by means of computers.
Chemoinformatics represents a vital link between experiment and theory in the area of drug design, through the extraction of information from data and conversion into knowledge. With the explosion of publicly available genomic information, such as that resulting from the Human Genome Project, in the middle of the 1990s, bioinformatics has become very popular not only in the scientific community but also among the general audience. This has led to the coining of the counterpart of bioinformatics in chemistry after about two decades as Chemoinformatics. However this field can actually be seen as about two hundred years old – ever since the first account of chemical data has been published in literature. Today’s technology in chemoinformatics in fact facilitates better organization, storage, retrieval and analysis of these data for further advanced predicting studies – thus, saving time and money, also possibly animal experiments, and advancing humankind by developing novel, and safer, drugs.
The last three decades have seen tremendous growth in this field with the advancement in the computer technologies. Today volumes and volumes of books has been written on this subject and even few text books available for teaching in universities at the BSc and MSc level. Though there are full time Masters degree programs available in universities abroad, in India this field has yet to get full recognition. Currently chemoinformatics is being introduced as part of an ongoing diploma or masters program in bioinformatics in spite of its maturity as a new discipline. Besides the traditional mainstream areas of chemoinformatics such as :
- database systems,
- computer-assisted structure elucidation systems,
- computer-assisted synthesis design systems, and
- quantitative structure-activity relationship (QSAR) etc
- in silico library design,
- virtual screening,
- docking studies (to mimmic Protein-small molecules interactions in biological systems),
- prediction of ADME (Absorption, distribution, metabolism and excretion) and toxicity.
Chemistry has already evolved from largely a study of the elements to a study of molecules to currently a study of molecular interactions, especially those involving biological macromolecules – the molecules such as proteins and sugars we humans are made of. This offers a excellent opportunity for chemoinformatics to grow in this new direction. The main focus of recently identified “cyber enabled chemistry” by the US National Science Foundation is on the development of integrated databases, data mining tools, molecular visualization and computational capabilities and the remote and networked use of instrumentation.
The scope of this rapidly developing field will certainly continue to expand. It is worth mentioning that there is a new trend of integration of chemoinformatics with bioinformatics. This is because many sectors of the chemical and pharmaceutical industries are interdisciplinary by nature, and major progress and developments in those industries are occurring in both bioinformatics and chemoinformatics side by side. Chemists will become more and more computer dependent, Internet dependent and chemoinformatics dependent.
Chemoinformatics through its development in the past half a century, has reached in the present wide acceptance, and will have a bright future! The purpose of this particular article is to highlight the various research and job opportunities available to a new generation of students in chemistry, computer science and biology at various levels in both academic and pharmaceutical environment.
Job Title of Recent Graduates
Graduates from the MSc in Chemoinformatics have taken up a variety of different types of posts upon starting employment. Examples of the job titles of recent graduates are given below: Chemoinformatics Scientist, Computational Chemist, Chemical Data Scientist, Regulatory Affairs Officer, Senior Information Analyst, Information Officer, Data Officer, Graduate IT Trainee, Programmer, QSAR Software Tester, Support Analyst, Business Analyst, Technical Editor, Consultant, Research Assistant Organizations/Companies of Recent Graduates etc., Graduates from the MSc in Chemoinformatics obtain posts with a wide range of organizations and companies.
Current positions in Chemoinformatics:
(Apply Now for Project Assistant : BE/BTech/MS bioinformatics, comp. Last date 16/6/11 click here)
Some of the companies sponsoring chemoinformatics products and activities include:
[Career opportunities in Chemoinformatics : Sales, Product development, use, research]
* Accelrys
* ACD/Labs (Advanced Chemistry Development, Inc.)
* Afferent Systems Inc.
* Agilent Technologies
* Aureus Pharma
* Barnard Chemical Information Ltd. (John Barnard and Geoff Downs) SEE: digital chemistry
* Bio-Rad Laboratories
* BioReason
* BioSolveIT
* BlueObelisk.org
* Bruker Daltonics Inc.
* Cambridge Crystallographic Data Centre
* CambridgeSoft Corporation
* CARB Center for Advanced Research in Biotechnology (NIST/University of Maryland)
* Cengent Therapeutics (Genes to Leads). Acquired by Inncardio, Inc.
* Center for Molecular Modeling (NIH)
* Centre for Molecular and Biomolecular Informatics CMBI
* Cerep
* ChemAxon
* ChemDiv, Inc. (Chemical Diversity)
* Chemical Abstracts Service
* Chemical Computing Group, Inc.
* Chemical Simulations Group
* ChemInnovation Software
* ChemNavigator
* ChemSW (Chemistry Software for Windows, formerly: WindowChem)
* Chenomx Inc.
* CIS Chemical Information System
* CombiChem.net
* CompuChem
* CrossFire Beilstein
* CSA Cambridge Scientific Abstracts
* Daylight Chemical Information Systems
* Derwent (Thomson)
* Dialog (Thomson)
* digital chemistry (formerly BCI, Barnard Chemical Information)
* Drug Design Methodologies
* eduSoft (Glen E. Kellogg, Donald J. Abraham) (hint!, molconn-z, HASL)
* Eidogen-Sertanty
* Elsevier MDL
* European Bioinformatics Institute (EMBL)
* FamilyGenetix (formerly, Cherwell Scientific) (Cyrillic, ModelMaker, Modelmanager)
* FIZ Chemie Berlin (Fachinformationszentrum Chemie GmbH)
* Fujitsu (CAChe)
* Gaussian
* GCC GenChemiCs (William J. (Bill) Welsh)
* gNova Scientific Software
* GridChem
* Hypercube, Inc.
* Iconix Pharmaceuticals
* IDBS
* Incyte
* InforSense (ChemSense, InforSense KDE)
* Inpharmatica Ltd. (Biopendium, Chematica)
* Invitrogen (Vector NTI)
* IOS Improved Outcomes Software (GeneLinker)
* ISI Web of Knowledge (Thomson Scientific)
* Jubilant Biosys
* Knovel
* LabVantage
* LabWare
* LeadScope, Inc.
* Lhasa Limited
* LION bioscience
* Matrix Science
* MEDIT – Molecular Extended Distribution in Information Technology
* Metaphorics, LLC
* Modgraph Consultants, Ltd.
* Molecular Connections (Netpro)
* Molecular Discovery
* Molecular Networks
* Molecular Solutions (Recruiting Company for computational chemistry and informatics)
* Molegro
* Molinspiration
* MolMine Bioinformatics Software Solutions
* Molsearch
* MolSoft (ICM)
* NCBI US National Center for Biotechnology Information
* New River Kinematics (MoluCAD)
* NLM US National Library of Medicine
* OpenEye Scientific Software
* Ovid
* Pharma Algorithms
* Princeton Simulations (Conformer)
* Proteome Systems
* Q-Chem, Inc.
* Questel/Orbit, Inc.
* Rosetta Biosoftware
* Schrödinger
* SciTegic
* Semantic Laboratories
* SemiChem (AMPAC, Codessa)
* Serena Software, Inc. (Pcmodel)
* STN
* Sunset Molecular Discovery, LLC
* Symyx Technologies
* TDS Technical Database Services, Inc. (DIPPR/EHS, COSMOtherm, LogKOW)
* TimTec
* Tripos
* Waters (Empower, NuGenesis, MassLynx)
* Wavefunction (Spartan)
* Wiley-VCH Publishers
* WinMOPAC (Fujitsu)
Chemoinformatics helped to answer some of the fundamental questions.
Are you still synthesizing a new compound?
Are you sure it is novel and not yet reported from 20+ million publications and 5+ million chemical patents?
Are you interested to publish / patent the molecule?
Are you aware of the physico-chemical, biological properties?
Can you search Chemical structures with the aid of Robots? or Search Engines?
What is the source / resource of chemical information Search? (Scifinder or Google?)
What is the next 'billion dollar' molecule waiting in the laboratory?
First Chemoinformatics conference in India was conducted at National Chemical Laboratory (21-23 Jan 2007) with the participation and presentation by eminent scientists like Prof. Alex Tropsha, Prof, J Gasteiger etc., Later published few selected papers highlighting the importance of open-source tools like chemxtreme, Chemstar, ChemScreener etc..,
With this background of past three decades, I decided to write a blog on chemistry for the benefit of society.
..Continue to read
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