Friday, September 22, 2006
Dr. KESHAB SHRESTHA
DETAILS SOON-
President, Dr. Keshab Shrestha Associate Professor/NHM.
Executive commitee members and advisory members of CENEED, Nepal
http://www.ceneed.org/executive_commitee.htm
BOOKS BY HIM
1. Keshab Shrestha 1998, Dictionary of Nepalese Plant Names, Mandala Book point, Kathmandu, Nepal.
IN MEDIA
1. FROM NEPAL NEWS.COM
IUCN rises up to document invasive alien species of flora
By Damaru Lal Bhandari
KATHMANDU, Oct 30: Come December the Nepal office of the International Union of Conservation of Nature (IUCN) will embark on a study on invasive alien species (IAS) of plants. IAS are species of organisms, which have been moved to a new habitat and are known to harm the ecosystems.
The study will be conducted in selected locations of Gandaki, Koshi and Karnali river basins from December. Which means IUCN staff shall lead local environmental activists, environmental organisations and school students in identifying IAS and draw up theinventory.
"Once we have the inventory we can launch campaign aimed at raising awareness about alien species among farmers and institutions involved in conservation efforts," said Sagendra Tiwari, programme co-ordinator of IUCN-Nepal. The study shall also focus on the ways the local people have tended to receive them.
"The vital purpose, of course, is to ascertain the way the farmers and conservationists have tended to cope with them and loss incurred by them," said Tiwari, adding additional concern is to find out their adverse impact on agriculture, forestry and fishery.
The intervention from IUCN comes in the wake of claims that native species of vegetation and habitats were facing threat from scores of alien species of plants. More common to the city dweller is water hyacinth, which can be seen spreading out over abandoned ponds of the Kathmandu Valley.
But Nepal Agriculture Research Council (NARC) has advised caution before damning the species as "alien." " We must concentrate on eking out benefits from them rather then saying they don’t belong here," said Bimal Kumar Baniya, a NARC officer.
He, however, conceded that some of the species like mikania micrantha, known locally as banmara, were really aggressive but "still do not make a case for disowning them."
" We are not yet in a position to correctly judge the scenario. But the problem with certain alien species is they predominate over local species, culminating in their eventual extinction," Tiwari further said.
In fact, it was Tiwari who drew up an inventory of IAS of plants based on review of literature. There are nearly 80 species, 10 of them most pervasive.
"Foreign plants like water hyacinth casts adverse impact on fish ponds," said Dharani Man Singh, Fisheries Development Officer associated with Fisheries Development Directorate.
Singh, however, hastened on to add," We have introduced Chinese grass carp. It is a fish which feeds on water hyacinth ruling out its growth. This is the strategy we have followed to protect fish ponds."
Dr. Keshab Shrestha, Director of Natural History Museum, has appreciated the efforts coming from IUCN on the issue of alien invasive species of plants.
"Of course, they are doing a good job. But still what we can say is the study is restricted to enumerating the species rather than eradicating them," he said. He also stressed the need to popularise indigenous species of flowering and decorative plants.
As Tiwari said, " We have decided to exercise restraint before damning them. We are conducting a study, which will be followed by recommendation."
However, species which fall under Sino-Japanese, South East Asian, Indian, African-Asian desert, Irano-Turranean and Central Asiatic region are not considered as alien to Nepal.
President, Dr. Keshab Shrestha Associate Professor/NHM.
Executive commitee members and advisory members of CENEED, Nepal
http://www.ceneed.org/executive_commitee.htm
BOOKS BY HIM
1. Keshab Shrestha 1998, Dictionary of Nepalese Plant Names, Mandala Book point, Kathmandu, Nepal.
IN MEDIA
1. FROM NEPAL NEWS.COM
IUCN rises up to document invasive alien species of flora
By Damaru Lal Bhandari
KATHMANDU, Oct 30: Come December the Nepal office of the International Union of Conservation of Nature (IUCN) will embark on a study on invasive alien species (IAS) of plants. IAS are species of organisms, which have been moved to a new habitat and are known to harm the ecosystems.
The study will be conducted in selected locations of Gandaki, Koshi and Karnali river basins from December. Which means IUCN staff shall lead local environmental activists, environmental organisations and school students in identifying IAS and draw up theinventory.
"Once we have the inventory we can launch campaign aimed at raising awareness about alien species among farmers and institutions involved in conservation efforts," said Sagendra Tiwari, programme co-ordinator of IUCN-Nepal. The study shall also focus on the ways the local people have tended to receive them.
"The vital purpose, of course, is to ascertain the way the farmers and conservationists have tended to cope with them and loss incurred by them," said Tiwari, adding additional concern is to find out their adverse impact on agriculture, forestry and fishery.
The intervention from IUCN comes in the wake of claims that native species of vegetation and habitats were facing threat from scores of alien species of plants. More common to the city dweller is water hyacinth, which can be seen spreading out over abandoned ponds of the Kathmandu Valley.
But Nepal Agriculture Research Council (NARC) has advised caution before damning the species as "alien." " We must concentrate on eking out benefits from them rather then saying they don’t belong here," said Bimal Kumar Baniya, a NARC officer.
He, however, conceded that some of the species like mikania micrantha, known locally as banmara, were really aggressive but "still do not make a case for disowning them."
" We are not yet in a position to correctly judge the scenario. But the problem with certain alien species is they predominate over local species, culminating in their eventual extinction," Tiwari further said.
In fact, it was Tiwari who drew up an inventory of IAS of plants based on review of literature. There are nearly 80 species, 10 of them most pervasive.
"Foreign plants like water hyacinth casts adverse impact on fish ponds," said Dharani Man Singh, Fisheries Development Officer associated with Fisheries Development Directorate.
Singh, however, hastened on to add," We have introduced Chinese grass carp. It is a fish which feeds on water hyacinth ruling out its growth. This is the strategy we have followed to protect fish ponds."
Dr. Keshab Shrestha, Director of Natural History Museum, has appreciated the efforts coming from IUCN on the issue of alien invasive species of plants.
"Of course, they are doing a good job. But still what we can say is the study is restricted to enumerating the species rather than eradicating them," he said. He also stressed the need to popularise indigenous species of flowering and decorative plants.
As Tiwari said, " We have decided to exercise restraint before damning them. We are conducting a study, which will be followed by recommendation."
However, species which fall under Sino-Japanese, South East Asian, Indian, African-Asian desert, Irano-Turranean and Central Asiatic region are not considered as alien to Nepal.
Wednesday, September 20, 2006
BALRAM K BHATTA
Email:
1. Bhatta BK, Osono T, Ishikawa H, Takeda H. Soil microfungi and soil nutrients as indicators of a pine plantation and an adjacent natural forest. European Journal of Soil Biology .
2 大園享司・Balram K. Bhatta ミズキ落葉の分解にともなう葉圏菌類の遷移 日本生態学会第50回大会(ポスター講演)つくば国際会議場 2003年3月
3. Osono T., Bhatta, B.K. & Takeda H. (2004) Phyllosphere fungi on living and decomposing leaves of giant dogwood. Mycoscience 45: 35-41.
4. Muneto Hirobe, John Sabang, Balram K. Bhatta, et al. Leaf-litter decomposition of 15 tree species in a lowland tropical rain forest in Sarawak: decomposition rates and initial litter chemistry Ref: http://www.frienvis.nic.in/con_fj/jounralofforestresearch[9](4).htm
5.
Details will be posted soon.
-Ed
1. Bhatta BK, Osono T, Ishikawa H, Takeda H. Soil microfungi and soil nutrients as indicators of a pine plantation and an adjacent natural forest. European Journal of Soil Biology .
2 大園享司・Balram K. Bhatta ミズキ落葉の分解にともなう葉圏菌類の遷移 日本生態学会第50回大会(ポスター講演)つくば国際会議場 2003年3月
3. Osono T., Bhatta, B.K. & Takeda H. (2004) Phyllosphere fungi on living and decomposing leaves of giant dogwood. Mycoscience 45: 35-41.
4. Muneto Hirobe, John Sabang, Balram K. Bhatta, et al. Leaf-litter decomposition of 15 tree species in a lowland tropical rain forest in Sarawak: decomposition rates and initial litter chemistry Ref: http://www.frienvis.nic.in/con_fj/jounralofforestresearch[9](4).htm
5.
Details will be posted soon.
-Ed
HOM BAHADUR RIZAL
References
A.
http://read.jst.go.jp/ddbs/plsql/KNKY_EG_24?code=1000311901
Revised Date: 2002.12.10
Researcher Name: RIJAL Hom (Bahadur)
Date of Birth: 1969.8
Organization Name: Kyoto University Graduate School of Engineering Department of Global Environment Engineering
Title: Graduate Student
Mailing Address: Yoshidahonmachi, Sakyo-ku, Kyoto-shi, Kyoto 606-8501 Japan
E-mail: ue.rijal@archi.kyoto-u.ac.jp
Code F: 1.442
Building Science and Building Equipment :THERMAL ENVIRONMENT OF NEPALESE TRADITIONAL HOUSES
Keyword showing a research field:THERMAL ENVIRONMENT OF NEPALESE TRADITIONAL HOUSES
Current research topic
1.
INVESTIGATION AND EVALUATION ON THERMAL ENVIRONMENT OF TRADITIONAL VERNACULAR HOUSES IN NEPALNEPAL,TRADITIONAL VERNACULAR HOUSES,EVALUATION OF THERMAL ENVIRONMENT
Cord F: 442 . Building Science and Building Equipment (Collaboration in Organization)
2.
A.
http://read.jst.go.jp/ddbs/plsql/KNKY_EG_24?code=1000311901
Revised Date: 2002.12.10
Researcher Name: RIJAL Hom (Bahadur)
Date of Birth: 1969.8
Organization Name: Kyoto University Graduate School of Engineering Department of Global Environment Engineering
Title: Graduate Student
Mailing Address: Yoshidahonmachi, Sakyo-ku, Kyoto-shi, Kyoto 606-8501 Japan
E-mail: ue.rijal@archi.kyoto-u.ac.jp
Code F: 1.442
Building Science and Building Equipment :THERMAL ENVIRONMENT OF NEPALESE TRADITIONAL HOUSES
Keyword showing a research field:THERMAL ENVIRONMENT OF NEPALESE TRADITIONAL HOUSES
Current research topic
1.
INVESTIGATION AND EVALUATION ON THERMAL ENVIRONMENT OF TRADITIONAL VERNACULAR HOUSES IN NEPALNEPAL,TRADITIONAL VERNACULAR HOUSES,EVALUATION OF THERMAL ENVIRONMENT
Cord F: 442 . Building Science and Building Equipment (Collaboration in Organization)
2.
Dr. SHANTA KARKI
शान्ता कार्की
Nepal add: POBox 15142, KPC 432, Kathmandu, Nepal
Kyodai entry: 2004/4
Graduation date: 2009/3/23
: Ph. D (Plant Breeding, Agriculture)
Research area: Plant Breeding (mPing transposon in Wild Oryza genus.)
Professional interests: Wild Oryza, Transposons, DNA sequencing and analysis, PCRs,
Current Add: Graduate school of Agriculture, laboratory of Plant Breeding, Kyoto University
Tel: 080-5306-4481
mailto:Email:shantakarki@rediffmail.com
References:
Copy the links and paste on the URL to check:
Analysis of distribution and proliferation of mPing family transposons in a wild rice (Oryza rufipogon Griff.)
http://www.jstage.jst.go.jp/article/jsbbs/59/3/297/_pdf
A. Kyoto University : http://www.ikushu.kais.kyoto-u.ac.jp/member.html
B.Aishwarya Vidya Padak to outstanding students: http://www.nepalnews.com.np/contents/englishdaily/ktmpost/2002/nov/nov09/local.htm
C.Gamma field symposium No 43:
http://www.nias.affrc.go.jp/newsletter/gfs/pdf/043.pdf
D 5th International Rice Genetics Symposium P143: page 181
http://www.irri.org/rg5/Abstracts.pdf
E. Home Page: http://shantakyoto.googlepages.com/
F: Publication: http://wwwsoc.nii.ac.jp/cssj/region/kinki/meeting_165.pdf
Nepal add: POBox 15142, KPC 432, Kathmandu, Nepal
Kyodai entry: 2004/4
Graduation date: 2009/3/23
: Ph. D (Plant Breeding, Agriculture)
Research area: Plant Breeding (mPing transposon in Wild Oryza genus.)
Professional interests: Wild Oryza, Transposons, DNA sequencing and analysis, PCRs,
Current Add: Graduate school of Agriculture, laboratory of Plant Breeding, Kyoto University
Tel: 080-5306-4481
mailto:Email:shantakarki@rediffmail.com
References:
Copy the links and paste on the URL to check:
Analysis of distribution and proliferation of mPing family transposons in a wild rice (Oryza rufipogon Griff.)
http://www.jstage.jst.go.jp/article/jsbbs/59/3/297/_pdf
A. Kyoto University : http://www.ikushu.kais.kyoto-u.ac.jp/member.html
B.Aishwarya Vidya Padak to outstanding students: http://www.nepalnews.com.np/contents/englishdaily/ktmpost/2002/nov/nov09/local.htm
C.Gamma field symposium No 43:
http://www.nias.affrc.go.jp/newsletter/gfs/pdf/043.pdf
D 5th International Rice Genetics Symposium P143: page 181
http://www.irri.org/rg5/Abstracts.pdf
E. Home Page: http://shantakyoto.googlepages.com/
F: Publication: http://wwwsoc.nii.ac.jp/cssj/region/kinki/meeting_165.pdf
ROSHAN KUMAR SHRESTHA
Address in Nepal: Chode Tole, Thimi
Kyoto University entry: October 2000
Kyoto University exited: June 2005
Total duration in Kyoto University : 4 years 9 months
Status: Research Student (Oct 2000 - Mar 2001)
M.Sc. Civil Engineering Student (Apr 2001 -Mar 2003)
Doctorate Urban and Environmental EngineeringStudent (Apr 2003 - May 2005)
Research area: Earth Surface Hydrology
Current Add: Minneapolis, Minnesota, USA
Tel: 612 623 8291
Email: roshanpost@yahoo.com
CLICK HERE TO KNOW HIM BETTER= http://www.geocities.com/roshanpost/index.html OR
http://www.geocities.com/roshanpost/index.html
REFERENCES
A. Congrat Dr. Roshan Shrestha
Dr. Roshan Kumar Shrestha has been honored with the Young Author Excellent Paper Award 2005 by the Japan Society of Hydrology & Water Resources, JSHWR. This award has been given for his paper entitled Performance Analysis of Different Meteorological Data and Resolutions Using MaScOD Hydrological Model Printed in Hydrological Processes. The award will be formally given on August 4, 2005 amid a function.
This award is given every year to one researcher under 35 who has published papers in JSHWR publications and its affiliated publications in that year. Eligible competitors for this award include associate professors, assistant professors, research associates, post doctoral researchers and company researchers under 35. This is the first time, this award has been given to a non-Japanese.
A native of Thimi, Khwopa, 33 year old Dr. Shrestha now works for a NASA funded project on global precipitation measurement by satelite observation, in the capacity of Research Associate in University of Minnesota, USA.
NESOCA Nepal extends its warmest filicitation to Dr. Shrestha for being honored with the above award and wishes every success in his new responsibility.
Here is his email address for those who wish to send congratulat0ry messages to him : roshanpost@gmail.com.
B.
RIPENDRA AWAL
Ripendra on left.
References:
A.
Ripendra Awal (Nepal)
"Floodplain Analysis and Risk Assessment of Lakhandei River"
The Lakhandei river basin is located in Sarlahi district of Central Development Region of Nepal. This river, originates in the eastern Siwalik Hills, is one of the most flood prone rivers in the country because of flash flood during monsoon rainfall. The huge loss of life and damage to properties during floods in 1993, 1995 and 1997 necessitate for the flood plain analysis and risk assessment of this river.
Floodplain analysis and risk assessment involves the study of complex interaction of hydraulics of the river flow with topographical and land use features of the floodplains. This study will use the one-dimensional numerical model HEC-RAS, ArcView GIS and HEC-GeoRAS extension for ArcView GIS will be used as an interface between the two systems for the pre-processing and post-processing of the data. Spatial analysis functionality of the GIS will be used for risk assessment. The attempt will also be made for floodplain analysis by using two-dimensional flow model FESWMS-2DH for comparative study.
The methodology for flood risk assessment will follow the approach developed by Gilard (1996). For the visualization of the results, maps are also prepared for different return periods. This will serve as an effective and efficient decision making tool which will help administrators and planners to identify areas of risk and prioritize their mitigation/response efforts, and it will also help to general public be aware of the flood risk and prepare for mitigation activities.
"Floodplain Analysis and Risk Assessment of Lakhandei River"
The Lakhandei river basin is located in Sarlahi district of Central Development Region of Nepal. This river, originates in the eastern Siwalik Hills, is one of the most flood prone rivers in the country because of flash flood during monsoon rainfall. The huge loss of life and damage to properties during floods in 1993, 1995 and 1997 necessitate for the flood plain analysis and risk assessment of this river.
Floodplain analysis and risk assessment involves the study of complex interaction of hydraulics of the river flow with topographical and land use features of the floodplains. This study will use the one-dimensional numerical model HEC-RAS, ArcView GIS and HEC-GeoRAS extension for ArcView GIS will be used as an interface between the two systems for the pre-processing and post-processing of the data. Spatial analysis functionality of the GIS will be used for risk assessment. The attempt will also be made for floodplain analysis by using two-dimensional flow model FESWMS-2DH for comparative study.
The methodology for flood risk assessment will follow the approach developed by Gilard (1996). For the visualization of the results, maps are also prepared for different return periods. This will serve as an effective and efficient decision making tool which will help administrators and planners to identify areas of risk and prioritize their mitigation/response efforts, and it will also help to general public be aware of the flood risk and prepare for mitigation activities.
or: http://www.proventionconsortium.org/?pageid=41®ionid=20&winnerid=74
B.. http://water.nml.uib.no/researcher/?id=1066
PADMA BAHADUR SHAHI
Dr. Padma Bahadur Shahi
Nepal add: Ramghat-5, Surkhet
Kyodai entry: October, 2003
Graduation date : September, 2005
Degree : Post Doctoral Fellowship, JSPS
Research area: Urban Transportation
Current Add: Kathmandu Engineering College, Kalimati, Kathmandu
Tel: 977-1-4284 902(O); 977-1-016211597 (R)
Email: pb_shahi@yahoo.com
References:
A.
Shahi Padma Bahadur & Aoyama Yoshitaka
“Costs, Economies of Scale, and Factor Demand in Urban Bus Transport”
Regional science association International ,
INTERNATIONAL SYMPOSIUM
and
37th ANNUAL CONFERENCE OF THE INDIAN REGIONAL SCIENCE ASSOCIATION
6 - 8 January 2006 At Indian Institute of Management Bangalore
Phone: +91 9343712880 (Mobile) Fax : +91-80-6584004, email: rsai2006@iimb.ernet.in Bannerghatta Road, Bangalore 560 076, India .
B. http://www.nepaljapan.com/view.php?section=showcontacts&ch=P
GOVINDA RIZAL
(in center)
Nepal add: Sundhara , Kathmandu,
Kyoto University entry: April 2005
Graduation date : March 2007 (Master), March 2010, Ph. D expected)
Degree : Masters Agriculture, (Plant Breeding)
Ph. D (expected by 2010 March)
Research area:
Ph. D.: Genetic control of proanthocyanidin and racal scavenging activites in soybean.
Masters: Improvement of Protein Quality in Soybean Through Gene Modification
Current Add: Kyoto Fu, Uji shi, Asakura, 50-1 NishiOkubo 22-205 (PC: 611-0033) Tel: 080 3812 9610
Email: govindarizal@gmail.com
Credits: http://rizag.blogspot.com/
Home Page: http://govindarizal.googlepages.com/
Editor and Academic program coordinator (2008-2009): Kyoto University, Organizing Committee for 10th Association for Pacific Rim Universities – Doctoral Students conference.
http://www.opir.kyoto-u.ac.jp/apru_dsc/index.html
Presentations
Kinki Crop Science Symposium, July 11, 2009, Kyoto University.
Japanese Society of Breeding, Annual Meeting, 2009, Tsukuba Japan, and Annual Meeting, 2008, Shiga, Japan.
The XVIIIth International Roundtable on Nucleoside, Nucleotides and Nucleic Acids, September 8- 11, 2008, Kyoto, Japan.
International Conference on Food Factors for Health Promotion (ICoFF2007), Nov 28-31, 2007, Kyoto International Conference Center, Kyoto, Japan.
The 3rd International Conference on Polyphenols and Health (ICPH 2007), November 25-28, 2007, Kyoto International Conference Center, Kyoto, Japan.
Plant Breeding Seminar, Yamagata, 2007
The 5th International Symposium of Rice Functional Genomics, October 15-17, 2007 at Epochal Tsukuba International Congress center, Tsukuba, Japan.
The 46th Gamma Field Symposium, 2007, Mito, Japan.
The 9th Kyoto University International Symposium: Integrating Global Environmental Studies towards
Human Security, June 22-23, 2007, Kyoto University, Kyoto, Japan
International Symposium on Pine Wilt Disease in Asia, Kyoto University, 15-17 February 2007, Kyoto Japan
United Nations University, seminar series on peace, Hokkaido, 2005
International Convention on Quality Control Management, Participatory Rural Appraisal (PRA)Training
Various seminars, symposiums and conferences related to Agriculture
Govinda Rizal
Nepal add: Sundhara , Kathmandu,
Kyoto University entry: April 2005
Graduation date : March 2007 (Master), March 2010, Ph. D expected)
Degree : Masters Agriculture, (Plant Breeding)
Ph. D (expected by 2010 March)
Research area:
Ph. D.: Genetic control of proanthocyanidin and racal scavenging activites in soybean.
Masters: Improvement of Protein Quality in Soybean Through Gene Modification
Current Add: Kyoto Fu, Uji shi, Asakura, 50-1 NishiOkubo 22-205 (PC: 611-0033) Tel: 080 3812 9610
Email: govindarizal@gmail.com
Credits: http://rizag.blogspot.com/
Home Page: http://govindarizal.googlepages.com/
Editor and Academic program coordinator (2008-2009): Kyoto University, Organizing Committee for 10th Association for Pacific Rim Universities – Doctoral Students conference.
http://www.opir.kyoto-u.ac.jp/apru_dsc/index.html
Presentations
Kinki Crop Science Symposium, July 11, 2009, Kyoto University.
Japanese Society of Breeding, Annual Meeting, 2009, Tsukuba Japan, and Annual Meeting, 2008, Shiga, Japan.
The XVIIIth International Roundtable on Nucleoside, Nucleotides and Nucleic Acids, September 8- 11, 2008, Kyoto, Japan.
International Conference on Food Factors for Health Promotion (ICoFF2007), Nov 28-31, 2007, Kyoto International Conference Center, Kyoto, Japan.
The 3rd International Conference on Polyphenols and Health (ICPH 2007), November 25-28, 2007, Kyoto International Conference Center, Kyoto, Japan.
Plant Breeding Seminar, Yamagata, 2007
The 5th International Symposium of Rice Functional Genomics, October 15-17, 2007 at Epochal Tsukuba International Congress center, Tsukuba, Japan.
The 46th Gamma Field Symposium, 2007, Mito, Japan.
The 9th Kyoto University International Symposium: Integrating Global Environmental Studies towards
Human Security, June 22-23, 2007, Kyoto University, Kyoto, Japan
International Symposium on Pine Wilt Disease in Asia, Kyoto University, 15-17 February 2007, Kyoto Japan
United Nations University, seminar series on peace, Hokkaido, 2005
International Convention on Quality Control Management, Participatory Rural Appraisal (PRA)Training
Various seminars, symposiums and conferences related to Agriculture
DUKKA BAHADUR KC
Dukka Bahadur K.C.
Kyoto university Entry: April 1997
Graduation Date: March 2006
DegreeObtained : B.Eng, M.Inf., D.Inf.Research
Area: Bioinformatics
Current Address: Atlanta, USA
NEpal Add: Satdobato, Lalitpur
email: dukkakc@gmail.com
REFERENCES
A.
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
Full text
Pdf (252 KB)
Source
ACM International Conference Proceeding Series; Vol. 55 archiveProceedings of the second conference on Asia-Pacific bioinformatics - Volume 29 table of contents
Dunedin, New Zealand
Pages: 191 - 200
Year of Publication: 2004
Authors
K. C. Dukka Bahadur
Kyoto University, Kyoto, Japan
Tatsuya Akutsu
Kyoto University, Kyoto, Japan
Etsuji Tomita
The University of Electro-Communications, Tokyo, Japan
Tomokazu Seki
The University of Electro-Communications, Tokyo, Japan
Publisher
Australian Computer Society, Inc. Darlinghurst, Australia, Australia
Additional Information:
abstract references index terms collaborative colleagues peer to peer
Tools and Actions:
Find similar Articles Review this Article Save this Article to a Binder Display Formats: BibTex EndNote ACM Ref
ABSTRACT
Protein side-chain packing has an important application in homology modeling, protein structure prediction, protein design, protein docking problems and many more.Protein side-chain packing problem is computationally known to be NP-hard (Akutsu, 1997) (Chazelle, Kingsford & Singh, 2003) (Pierce & Winfree, 2002). In the field of computer science, the notion of reduction of a problem to other problems is quite often used to design algorithms and to prove the complexity of a certain problem. In this work, we have used this notion of reduction to solve protein side-chain packing problem.We have developed a deterministic algorithm based approach to solve protein side-chain packing problem based on clique-based algorithms. For this, we reduced this problem to the maximum clique finding problem. Moreover, in order to incorporate the interaction preferences between the atoms, we have then extended this approach to maximum edge-weight clique finding problem by assigning weights based on probability discriminatory function. We have then solved this clique finding problem by using the clique finding algorithm developed by two of the authors (Tomita & Seki, 2003) and its variants (Suzuki, Tomita & Seki 2002).We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found considerable improvement in terms of the size of the proteins and in terms of the efficiency and accuracy of the prediction.
Kyoto university Entry: April 1997
Graduation Date: March 2006
DegreeObtained : B.Eng, M.Inf., D.Inf.Research
Area: Bioinformatics
Current Address: Atlanta, USA
NEpal Add: Satdobato, Lalitpur
email: dukkakc@gmail.com
REFERENCES
A.
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
Full text
Pdf (252 KB)
Source
ACM International Conference Proceeding Series; Vol. 55 archiveProceedings of the second conference on Asia-Pacific bioinformatics - Volume 29 table of contents
Dunedin, New Zealand
Pages: 191 - 200
Year of Publication: 2004
Authors
K. C. Dukka Bahadur
Kyoto University, Kyoto, Japan
Tatsuya Akutsu
Kyoto University, Kyoto, Japan
Etsuji Tomita
The University of Electro-Communications, Tokyo, Japan
Tomokazu Seki
The University of Electro-Communications, Tokyo, Japan
Publisher
Australian Computer Society, Inc. Darlinghurst, Australia, Australia
Additional Information:
abstract references index terms collaborative colleagues peer to peer
Tools and Actions:
Find similar Articles Review this Article Save this Article to a Binder Display Formats: BibTex EndNote ACM Ref
ABSTRACT
Protein side-chain packing has an important application in homology modeling, protein structure prediction, protein design, protein docking problems and many more.Protein side-chain packing problem is computationally known to be NP-hard (Akutsu, 1997) (Chazelle, Kingsford & Singh, 2003) (Pierce & Winfree, 2002). In the field of computer science, the notion of reduction of a problem to other problems is quite often used to design algorithms and to prove the complexity of a certain problem. In this work, we have used this notion of reduction to solve protein side-chain packing problem.We have developed a deterministic algorithm based approach to solve protein side-chain packing problem based on clique-based algorithms. For this, we reduced this problem to the maximum clique finding problem. Moreover, in order to incorporate the interaction preferences between the atoms, we have then extended this approach to maximum edge-weight clique finding problem by assigning weights based on probability discriminatory function. We have then solved this clique finding problem by using the clique finding algorithm developed by two of the authors (Tomita & Seki, 2003) and its variants (Suzuki, Tomita & Seki 2002).We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found considerable improvement in terms of the size of the proteins and in terms of the efficiency and accuracy of the prediction.
BINAYA RAJ SHIVAKOTI
Mr. Binaya Raj Shivakoti
Nationality: Nepal
Present Nationality: Nepal
School: School of Environment, Resources and Development
Program: Agricultural Systems and Engineering
Field of Study: Agricultural Machinery and Management
Degree: Master of Science
Graduation Year: 2004
Graduation Month: August
Email: binaya.dc@rceqm.mbox.media.kyoto-u.ac.jp
Office Address: Doctoral student
Research Center for Environmental Quality Mgmnt.
(RCEQM),Graduate School of Engineering,
Kyoto University,1-2 Yumihama,Otsu,
Shiga,520-0811
Japan
Tel.: +81-080-5302-4916
Fax: +81-77-524-9869
Home Address: Santosh Marg-308, New Baneswor-10
Kathmandu
Nepal
Tel.: 0977-1-4491631
Mailing Address: Office
Information from :
http://www.asdu.ait.ac.th/Alumni/AlumniByID.cfm?AlumniID=20040197
References Most of them in Japanese.
A. http://www.jswe-kansai.com/forum/program05.html
B. http://www.jsps.go.jp/j-bilat/core/data/07-1_jissi/MOE_kyoto.pdf
C. http://hes.pbh.med.kyoto-u.ac.jp/pfcreview/PFCpresen.html
D http://www.water.civil.tohoku.ac.jp/rr2002/member.html
E. http://www.eqc.kyoto-u.ac.jp/local/member.html
F. http://www.dipcon2006.itu.edu.tr/DipCon%20Program%20Final.pdf
Nationality: Nepal
Present Nationality: Nepal
School: School of Environment, Resources and Development
Program: Agricultural Systems and Engineering
Field of Study: Agricultural Machinery and Management
Degree: Master of Science
Graduation Year: 2004
Graduation Month: August
Email: binaya.dc@rceqm.mbox.media.kyoto-u.ac.jp
Office Address: Doctoral student
Research Center for Environmental Quality Mgmnt.
(RCEQM),Graduate School of Engineering,
Kyoto University,1-2 Yumihama,Otsu,
Shiga,520-0811
Japan
Tel.: +81-080-5302-4916
Fax: +81-77-524-9869
Home Address: Santosh Marg-308, New Baneswor-10
Kathmandu
Nepal
Tel.: 0977-1-4491631
Mailing Address: Office
Information from :
http://www.asdu.ait.ac.th/Alumni/AlumniByID.cfm?AlumniID=20040197
References Most of them in Japanese.
A. http://www.jswe-kansai.com/forum/program05.html
B. http://www.jsps.go.jp/j-bilat/core/data/07-1_jissi/MOE_kyoto.pdf
C. http://hes.pbh.med.kyoto-u.ac.jp/pfcreview/PFCpresen.html
D http://www.water.civil.tohoku.ac.jp/rr2002/member.html
E. http://www.eqc.kyoto-u.ac.jp/local/member.html
F. http://www.dipcon2006.itu.edu.tr/DipCon%20Program%20Final.pdf
DIWAKAR ACHARYA
Diwakar Acharya
Nepal add: Kalimatidol Kathmandu-9, KathmanduKyodai entry date: April 2006
Status: Visiting Lecturer
Research area: Sanskrit and Indological Studies
Current Add: Kitashirakawa Shibuse cho 68, Sakyo ku, Kyoto 606-8283
Tel: 075-753-2803 (office) 075-702-9519 (home)
Email:acharyadiwakar@ hotmail.com
Address
Diwakar Acharya
Graduate School of Letters
Kyoto University
Yoshida Honmachi, Sakyo-ku
Kyoto 606-8501, Japan
Tel.: +81 75 753 2803
References:
A।Staff of NGMCP http://www.uni-hamburg.de/ngmcp/staff.html
। http://www.jainheritagecentres.com/chaturmas1/chaturmassthanak.html
12th WORLD SANSKRIT CONFERENCE Helsinki, Finland, 13-18 July, 2003 : http://www।helsinki.fi/hum/aakkl/12wsc/participants.html
If you can decipher Japanese
http://www।hmn.bun.kyoto-u.ac.jp/vaada/announcement.html
In Japanese : http://www।hmn.bun.kyoto-u.ac.jp/vaada/
http://indologica.blogg.de/eintrag.php?id=1006
http://www.tantric-studies.org/people/diwakar-acharya/
http://www.amazon.ca/Little-Clay-Cart-Shudraka-Acharya/dp/0814707297
http://www.springerlink.com/content/94572h3q26v0x852/
http://www.bun.kyoto-u.ac.jp/indology/index_e.html
http://www.tantric-studies.org/projects/early-tantra/1iwet/
http://www.soas.ac.uk/research/publications/journals/ijjs/archive/
www.csh-delhi.com/publications/downloads/pattrika/pattrika29.pdf
www.ifpindia.org/Melanges-tantriques-a-la-memoire-d-Helene-Brunner-Tantric-Studies-in-Memory-of-Helene-Brunner.html
iriab.soka.ac.jp/orc/pdf/ARIRIAB-09-Contents.pdf
www.sub.uni-goettingen.de/ebene_1/fiindolo/gretil/1_sanskr/6_sastra/3_phil/vedanta/mbrahsiu.htm
www.hindu.com/2007/01/11/stories/2007011102800200.htm
http://www.uni-hamburg.de/ngmcp/staff_e.html
http://www.uni-hamburg.de/ngmcp/publications_e_print.html
www.buddhismuskunde.uni-hamburg.de/fileadmin/pdf/digitale_texte/Bd11-K06Acharya.pdf
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