The National University of Malaysia Pusat Perubatan Universiti Kebangsaan Malaysia is located in Cheras and also has a branch campus in Kuala Lumpur. There are 17,500 undergraduate students enrolled, and 5,105 postgraduate students of which 1368 are foreign students from 35 countries.Universiti Kebangsaan Malaysia is one of five research universities in the country. It was ranked number 259th in the world by QS World University Rankings in 2014. It is ranked 98th place in the 100 best new universities established within the last 50 years in the world. It is the only university from Malaysia that made it in the 2012 Quacquarelli Symonds Top 50 Universities Under 50 Years Old list ranked in the 31st place. It placed 53rd and 58th in the QS Top 500 Asian University Rankings in 2011 and 2012 respectively. Wikipedia.
News Article | April 28, 2017
Tamim Chalati remembers an Aleppo where you could get pizza at 3am. “I had a good salary and social life,” the scientist says, recalling how he used to take his two children out for “hot and crispy barbecue food”, their favourite, several times a week. They lived a comfortable life, with his wife a doctor, and he head of the Department of Pharmaceutics and Pharmaceutical Technology at the University of Aleppo. When war broke out in 2011, first only cracks appeared in Chalati’s world – the electricity would go off, they’d be without water for a few days. But on one summer day in 2012, they found the streets empty and the hospital closed. “We then saw many people walking west [away from a battle in the eastern part of the city], and they told us the war had reached us.” That night there were air strikes, and the family watched in horror as the security situation spiralled out of control, food became scarce and the value of money plummeted. Only 10 students out of 100 were now attending his classes, and when by the end of the year many colleagues had left the country, Chalati and his wife debated if they should too. But they held out until January 2013, when two blasts at the University of Aleppo killed 80 people. Chalati was in his office. His mind went immediately to his children, who were in school, just a few kilometres from the blast. “I couldn’t reach [them] to find out if they were still alive – it was really terrible,” he says. They were safe, but one of the explosions destroyed the kiosk where he often picked up coffee on the school run. The academic began frantically applying for positions at universities in Turkey, Jordan and the UAE – any posting that could give his family a route out of Syria. There would be another two tense years before he finally secured a fellowship through the Institute of International Education’s (IIE) Scholar Rescue Fund. Today the Chalitis are living in England and he is a research associate in the chemistry department at the University of York. Chalati is one of the lucky ones. The IIE, which has helped rescue persecuted scholars since 1919, currently has an acceptance rate of less than 20% for qualified Syrian scholars. It is not the only organisation offering support to academics in danger, but “the needs still far outstrip the resources available,” says James King, assistant director of the Scholar Rescue Fund. The organisation estimates that among the millions who fled Syria there are 2,000 university professionals. Many are still stuck in makeshift camps, and even if resettled, are unable to work. They fly under the radar as academics are not considered one of the most at-risk refugee groups. Yet more than 450 have been assassinated in Iraq since 2003, and an analysis by Scholars at Risk of 158 reported attacks against university professionals in 35 countries from May 2015 to September 2016 found threats ranged from travel restrictions to wrongful prosecutions, forced disappearances and murder. “Scholars, scientists and human rights activists are targeted from every direction,” says Radwan Ziadeh, a senior analyst at the Arab Centre in Washington DC. He should know – the former dentist left Syria in 2007 after receiving threats from the Assad’s security forces after calling for government reform, and he’s currently on an Isis kill list. His asylum case in the US has been pending for three years. So why don’t host countries do more to make the most of these scientists, medics, engineers and other skilled workers? “The main obstacle is the lack of political will, with the rise of the populist movements around the world,” Ziadeh says, explaining that politicians too often treat refugees as a homogenous group. King thinks that a lack of awareness about their educational qualifications, as well as practical challenges related to cost, language barriers, and qualifications assessment, are issues. “Governments and higher education institutions are beginning to recognise the opportunity here,” he says. “But we have a real responsibility to ensure that refugee scientists are supported to continue their academic work because these are the very individuals who will be rebuilding their countries, who will build healthy diaspora communities, and who will really contribute to their host communities.” Chalati experienced the issue of getting his qualifications recognised first-hand. He has a master’s and PhD from a French university but his BA in pharmacy is from a Syrian university, so in the UK he cannot be employed permanently at a school of pharmacy, unless he redoes some exams – a process that could take three years. “In Syria I was a senior academic, but when I came to the UK I had to start from scratch as a postdoc, as if the previous five years of my career did not exist,” he says. Still, scientific institutions can play an important role in helping refugee scientists integrate into their new communities. “Our scholars often don’t consider themselves refugees: when they are integrated into a lab they’re scientists again, and it’s very important for them to be able to move beyond this reductionist label of refugee,” King says. In March, a workshop was convened by The World Academy of Sciences (TWAS) to discuss how to better support refugee scientists. They recommended that scientific communities establish relations with refugee processing centres, and that host governments accelerate the approval of asylum applications from scientists. TWAS also discussed how to rebuild scientific communities in countries returning to stability, suggesting governments provide tax exemptions and laboratory facilities to persuade skilled workers to return. Eqbal Mohammed Dauqan, a Yemeni scientist now on a scholarship at the National University of Malaysia, is sceptical about these recommendations. In March 2015, she was head of the medical laboratory sciences department at Al-Saeed University of Taiz, but had spent eight months without the internet, electricity or salary, and a bomb hit her house. “When students and researchers finish their fellowships how are they coming back here?” she says. “We don’t even have an airport, and even if they [get here] they are not going to have a stipend for research, because what remains of the government has no money.” Personally, she is not sure of what her next move should be – her scholarship will run out in 2018. “Now I am not a refugee scientist, I am a visiting scholar, but maybe I’ll be a refugee next year.” Join our community of development professionals and humanitarians. Follow @GuardianGDP on Twitter.
News Article | April 20, 2017
Shari M. Ling, MD has been selected to receive the first-ever Public Service Award from NKF, established to honor those who have dedicated their careers to public service and who have helped to shape public policies or government programs that improve outcomes for kidney patients. Dr. Ling currently serves as the Deputy Chief Medical Officer for the Centers for Medicare and Medicaid Services (CMS) and Medical Officer in the Center for Clinical Standards and Quality (CCSQ). In her role at CMS, she assists the CMS Chief Medical Officer in the agency's pursuit of better health care, healthier populations and smarter spending. Dr. Ling's committed focus is on the achievement of meaningful health outcomes for patients and families through the delivery of high quality, person-centered care, across all care settings. Her clinical focus and scientific interest is in the care of persons with dementia, multiple chronic conditions and functional limitations. Derek Forfang, a kidney patient and long-time kidney disease advocate, has been selected to receive the first-ever Celeste Castillo Lee Patient Engagement Award, established in honor of Celeste Castillo Lee, a longtime advocate for patient-centered care and empowerment. It is the highest honor given by NKF to a distinguished kidney patient who exemplifies NKF's mission and Celeste's legacy of putting patients at the center of all aspects of healthcare through their involvement with NKF and community partners. Mr. Forfang, of San Pablo, California, has been an end-stage renal disease (ESRD) patient since 1999. He received a kidney transplant and has also been on peritoneal dialysis and hemodialysis. A regional leader of NKF's Kidney Advocacy Committee and a member of the Public Policy Committee, Derek has worked tirelessly to protect and improve care for the kidney community. Merck been selected to receive the 2017 Corporate Innovator Award which recognizes industry partners that advance the field of nephrology by addressing an unmet medical need, or improving upon an existing practice, therapeutic or technology. Merck's innovative new treatment for hepatitis C, ZEPATIER, is the only direct anti-viral agent specifically tested and approved for use in patients with chronic kidney disease stages four and five. Paul Palevsky, MD has been selected to receive the Dr. J. Michael Lazarus Distinguished Award established to honor Dr. Lazarus for his major contributions to the clinical science and care of dialysis patients, and to recognize individuals whose research has yielded novel insights related to renal replacement therapy. Dr. Palevsky is Professor of Medicine and Clinical and Translational Science in the Renal-Electrolyte Division at the University of Pittsburgh School of Medicine; and serves as Chief of the Renal Section at the VA Pittsburgh Healthcare System. Dr. Palevsky's research has primarily focused on acute kidney injury and critical care nephrology. He will be presenting the Lazarus lecture on "We Don't Have to Fail at Acute Renal Failure: A Multidisciplinary Approach to Quality Improvement" on Friday, April 21st at 8:45 a.m. at the NKF Spring Clinical Meetings. Susanne Nicholas, MD, MPH, PhD has been selected to receive the Medical Advisory Board Distinguished Service Award established to recognize an individual for their educational activities and community service in promoting the mission of NKF on a local level. Dr. Nicholas is a tenured Associate Professor of Medicine at UCLA in the Division of Nephrology where she maintains her clinical responsibilities, and the Division of Endocrinology, Diabetes and Hypertension, where she conducts research. She is also a Clinical Hypertension Specialist. Dr. Nicholas' research interests include understanding and identifying key factors that promote the pathogenesis of diabetic kidney disease (DKD); uncovering and validating novel biomarkers that may predict DKD progression; and quantifying renal structural changes associated with DKD in response to novel therapeutics, using stereology principles. Her research over the past 15 years has led to the identification of a novel biomarker of DKD, which is currently being validated in clinical studies. Katherine R. Tuttle, MD, FASN, FACP, FNKF, has been selected to receive the prestigious Garabed Eknoyan Award, created to recognize an individual who has promoted the mission of NKF in Making Lives Better for people with kidney disease through the exceptional contributions to key initiatives of NKF such as the Kidney Disease Outcomes Quality Initiative (KDOQI) or clinical research in the field of kidney disease. Dr. Tuttle is the Executive Director for Research at Providence Health Care in Spokane, and serves as Co-Principal Investigator of the Institute of Translational Health Sciences, Investigator at Kidney Research Institute, and Clinical Professor of Medicine for the University of Washington. Dr. Tuttle's major research interests include diabetic kidney disease, hypertension, renal vascular disease, nutrition in chronic kidney disease, and transitional care. She has chaired numerous workgroups focused on diabetes and kidney disease including NKF's KDOQI Workgroup for Diabetes and Chronic Kidney Disease. Jonathan Himmelfarb, MD has been selected to receive the Donald W. Seldin Award, established to recognize excellence in clinical nephrology in the tradition of one of the foremost teachers and researchers in the field, Dr. Donald W. Seldin. Dr. Himmelfarb is a Professor of Medicine, Director of the Kidney Research Institute, and holds the Joseph W. Eschbach, M.D. Endowed Chair in Kidney Research at the University of Washington School of Medicine. He is the author of more than 200 peer-reviewed publications, has served on numerous grant review committees and scientific advisory boards and has held leadership positions in many national and international nephrology societies. Dr. Himmelfarb has served on expert panels for the U.S. Food and Drug Administration, Veterans Health Administration, and Centers for Medicare & Medicaid Services. He is also a nephrologist who cares for patients with kidney disease, and an internationally recognized educator about kidney disease. Raymond R. Townsend, MD has been selected to receive the Shaul G. Massry Distinguished Lecture Award, established to honor Dr. Massry for his scientific achievements and contribution to the kidney health care community and to NKF. Dr. Townsend is Professor of Medicine and an Associate Director of the Center for Human Phenomic Studies at the University of Pennsylvania. He is currently a Principal Investigator evaluating the role of demographic, phenotypic, humoral and genetic factors in the progression of kidney disease and the development and progression of cardiovascular disease in patients with chronic kidney disease. He was also the Principal Investigator of a multicenter effort evaluating the specific role of pulse wave velocity in the renal and cardiovascular consequences of chronic kidney disease. Dr. Townsend led the work group that wrote the KDOQI Commentary on the 2012 KDIGO Guideline on this subject, and most recently co-chaired the NKF workshop on Potassium Homeostasis in Disease and Health, the report on which will soon be published in the American Journal of Kidney Disease and Journal of the American Society of Hypertension. Tilakavati Karupaiah, PhD, APD, AN has been selected to receive the Joel D. Kopple Award, an annual award honoring an individual who has made significant contributions to the field of renal nutrition. Dr. Karupaiah is an Accredited Practicing Dietitian with Dietitian's Association of Australia, a Professor and Head of the Dietetics Program at the National University of Malaysia; and also Adjunct Associate Professor at Wayne State University, Detroit. Dr. Karupaiah's involvement in renal nutrition began because of a lack of dietitians in this field in Malaysia, and dialysis patients needed patient-friendly information about local diets. At the National University of Malaysia, she encouraged early exposure of dietetic students to renal patient care through community engagement, outpatient counseling and practical skills on patient diet planning. Dr. Karupaiah is now targeting capacity building mentorship for developing renal dietitians in Malaysia through nutrition research. For the past 26 years, nephrology healthcare professionals from across the country have come to NKF's Spring Clinical Meetings to learn about the newest developments related to all aspects of nephrology practice, network with colleagues, and present their research findings. The NKF Spring Clinical Meetings are designed for meaningful change in the multidisciplinary healthcare teams' skills, performance, and patient health outcomes. It is the only conference of its kind that focuses on translating science into practice for the entire healthcare team. 1 in 3 American adults is at risk for kidney disease. 26 million American adults have kidney disease—and most aren't aware of it. Risk factors for kidney disease include diabetes, high blood pressure, family history, and age 60+. People of African American; Hispanic; Native American; Asian; or Pacific Islander descent are at increased risk for developing the disease. African Americans are 3 ½ times more likely, and Hispanics 1 ½ times more likely, to experience kidney failure. The National Kidney Foundation (NKF) is the largest, most comprehensive and longstanding organization dedicated to the awareness, prevention and treatment of kidney disease. For more information about NKF visit www.kidney.org. : Full press releases on each award recipient, including quotes for attribution, are hyperlinked by recipient's name and can also be found in the Newsroom at www.kidney.org. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/national-kidney-foundation-honors-leading-researchers-clinicians-patient-advocates-and-more-at-its-26th-annual-spring-clinical-meetings-300442333.html
Hatamlou A.,Islamic Azad University at Khoy |
Hatamlou A.,National University of Malaysia
Information Sciences | Year: 2013
Nature has always been a source of inspiration. Over the last few decades, it has stimulated many successful algorithms and computational tools for dealing with complex and optimization problems. This paper proposes a new heuristic algorithm that is inspired by the black hole phenomenon. Similar to other population-based algorithms, the black hole algorithm (BH) starts with an initial population of candidate solutions to an optimization problem and an objective function that is calculated for them. At each iteration of the black hole algorithm, the best candidate is selected to be the black hole, which then starts pulling other candidates around it, called stars. If a star gets too close to the black hole, it will be swallowed by the black hole and is gone forever. In such a case, a new star (candidate solution) is randomly generated and placed in the search space and starts a new search. To evaluate the performance of the black hole algorithm, it is applied to solve the clustering problem, which is a NP-hard problem. The experimental results show that the proposed black hole algorithm outperforms other traditional heuristic algorithms for several benchmark datasets. © 2012 Elsevier Inc. All rights reserved.
Agency: GTR | Branch: NERC | Program: | Phase: Research Grant | Award Amount: 1.30M | Year: 2013
Anthropogenic disturbance and land-use change in the tropics is leading to irrevocable changes in biodiversity and substantial shifts in ecosystem biogeochemistry. Yet, we still have a poor understanding of how human-driven changes in biodiversity feed back to alter biogeochemical processes. This knowledge gap substantially restricts our ability to model and predict the response of tropical ecosystems to current and future environmental change. There are a number of critical challenges to our understanding of how changes in biodiversity may alter ecosystem processes in the tropics; namely: (i) how the high taxonomic diversity of the tropics is linked to ecosystem functioning, (ii) how changes in the interactions among trophic levels and taxonomic groups following disturbance impacts upon functional diversity and biogeochemistry, and (iii) how plot-level measurements can be used to scale to whole landscapes. We have formed a consortium to address these critical challenges to launch a large-scale, replicated, and fully integrated study that brings together a multi-disciplinary team with the skills and expertise to study the necessary taxonomic and trophic groups, different biogeochemical processes, and the complex interactions amongst them. To understand and quantify the effects of land-use change on the activity of focal biodiversity groups and how this impacts biogeochemistry, we will: (i) analyse pre-existing data on distributions of focal biodiversity groups; (ii) sample the landscape-scale treatments at the Stability of Altered Forest Ecosystems (SAFE) Project site (treatments include forest degradation, fragmentation, oil palm conversion) and key auxiliary sites (Maliau Basin - old growth on infertile soils, Lambir Hills - old growth on fertile soils, Sabah Biodiversity Experiment - rehabilitated forest, INFAPRO-FACE - rehabilitated forest); and (iii) implement new experiments that manipulate key components of biodiversity and pathways of belowground carbon flux. The manipulations will focus on trees and lianas, mycorrhizal fungi, termites and ants, because these organisms are the likely agents of change for biogeochemical cycling in human-modified tropical forests. We will use a combination of cutting-edge techniques to test how these target groups of organisms interact each other to affect biogeochemical cycling. We will additionally collate and analyse archived data on other taxa, including vertebrates of conservation concern. The key unifying concept is the recognition that so-called functional traits play a key role in linking taxonomic diversity to ecosystem function. We will focus on identifying key functional traits associated with plants, and how they vary in abundance along the disturbance gradient at SAFE. In particular, we propose that leaf functional traits (e.g. physical and chemical recalcitrance, nitrogen content, etc.) play a pivotal role in determining key ecosystem processes and also strongly influence atmospheric composition. Critically, cutting-edge airborne remote sensing techniques suggest it is possible to map leaf functional traits, chemistry and physiology at landscape-scales, and so we will use these novel airborne methods to quantify landscape-scale patterns of forest degradation, canopy structure, biogeochemical cycling and tree distributions. Process-based mathematical models will then be linked to the remote sensing imagery and ground-based measurements of functional diversity and biogeochemical cycling to upscale our findings over disturbance gradients.
Siow K.S.,National University of Malaysia
Journal of Electronic Materials | Year: 2014
Silver (Ag) has been under development for use as interconnect material for power electronics packaging since the late 1980s. Despite its long development history, high thermal and electrical conductivities, and lead-free composition, sintered Ag technology has limited market penetration. This review sets out to explore what is required to make this technology more viable. This review also covers the origin of sintered Ag, the different types and application methods of sintered Ag pastes and laminates, and the long-term reliability of sintered Ag joints. Sintered Ag pastes are classified according to whether pressure is required for sintering and further classified according to their filler sizes. This review discusses the main methods of applying Ag pastes/laminates as die-attach materials and the related processing conditions. The long-term reliability of sintered Ag joints depends on the density of the sintered joint, selection of metallization or plating schemes, types of substrates, substrate roughness, formulation of Ag pastes/laminates, joint configurations (i.e., joint thicknesses and die sizes), and testing conditions. This paper identifies four challenges that must be overcome for the proliferation of sintered Ag technology: changes in materials formulation, the successful navigation of the complex patent landscape, the availability of production and inspection equipment, and the health concerns of Ag nanoparticles. This paper is expected to be useful to materials suppliers and semiconductor companies that are considering this technology for their future packages. © 2014 TMS.
Chowdhury R.H.,National University of Malaysia
Sensors (Basel, Switzerland) | Year: 2013
Electromyography (EMG) signals are becoming increasingly important in many applications, including clinical/biomedical, prosthesis or rehabilitation devices, human machine interactions, and more. However, noisy EMG signals are the major hurdles to be overcome in order to achieve improved performance in the above applications. Detection, processing and classification analysis in electromyography (EMG) is very desirable because it allows a more standardized and precise evaluation of the neurophysiological, rehabitational and assistive technological findings. This paper reviews two prominent areas; first: the pre-processing method for eliminating possible artifacts via appropriate preparation at the time of recording EMG signals, and second: a brief explanation of the different methods for processing and classifying EMG signals. This study then compares the numerous methods of analyzing EMG signals, in terms of their performance. The crux of this paper is to review the most recent developments and research studies related to the issues mentioned above.
Jie Y.,National University of Malaysia
Reviews of environmental contamination and toxicology | Year: 2013
In this review, our aim was to examine the influence of geographic variations on asthma prevalence and morbidity among adults, which is important for improving our understanding, identifying the burden, and for developing and implementing interventions aimed at reducing asthma morbidity. Asthma is a complex inflammatory disease of multifactorial origin, and is influenced by both environmental and genetic factors. The disparities in asthma prevalence and morbidity among the world's geographic locations are more likely to be associated with environmental exposures than genetic differences. In writing this article, we found that the indoor factors most consistently associated with asthma and asthma-related symptoms in adults included fuel combustion, mold growth, and environmental tobacco smoke in both urban and rural areas. Asthma and asthma-related symptoms occurred more frequently in urban than in rural areas, and that difference correlated with environmental risk exposures, SES, and healthcare access. Environmental risk factors to which urban adults were more frequently exposed than rural adults were dust mites,high levels of vehicle emissions, and a westernized lifestyle.Exposure to indoor biological contaminants in the urban environment is common.The main risk factors for developing asthma in urban areas are atopy and allergy to house dust mites, followed by allergens from animal dander. House dust mite exposure may potentially explain differences in diagnosis of asthma prevalence and morbidity among adults in urban vs. rural areas. In addition, the prevalence of asthma morbidity increases with urbanization. High levels of vehicle emissions,Western lifestyles and degree of urbanization itself, may affect outdoor and thereby indoor air quality. In urban areas, biomass fuels have been widely replaced by cleaner energy sources at home, such as gas and electricity, but in most developing countries, coal is still a major source of fuel for cooking and heating, particularly in winter. Moreover, exposure to ETS is common at home or at work in urban areas.There is evidence that asthma prevalence and morbidity is less common in rural than in urban areas. The possible reasons are that rural residents are exposed early in life to stables and to farm milk production, and such exposures are protective against developing asthma morbidity. Even so, asthma morbidity is disproportionately high among poor inner-city residents and in rural populations. A higher proportion of adult residents of nonmetropolitan areas were characterized as follows:aged 55 years or older, no previous college admission, low household income, no health insurance coverage, and could not see a doctor due to healthcare service availability, etc. In rural areas, biomass fuels meet more than 70% of the rural energy needs. Progress in adopting modern energy sources in rural areas has been slow. The most direct health impact comes from household energy use among the poor, who depend almost entirely on burning biomass fuels in simple cooking devices that are placed in inadequately ventilated spaces. Prospective studies are needed to assess the long-term effects of biomass smoke on lung health among adults in rural areas.Geographic differences in asthma susceptibility exist around the world. The reason for the differences in asthma prevalence in rural and urban areas may be due to the fact that populations have different lifestyles and cultures, as well as different environmental exposures and different genetic backgrounds. Identifying geographic disparities in asthma hospitalizations is critical to implementing prevention strategies,reducing morbidity, and improving healthcare financing for clinical asthma treatment. Although evidence shows that differences in the prevalence of asthma do exist between urban and rural dwellers in many parts of the world, including in developed countries, data are inadequate to evaluate the extent to which different pollutant exposures contribute to asthma morbidity and severity of asthma between urban and rural areas.
Karim N.A.,National University of Malaysia |
Kamarudin S.K.,National University of Malaysia
Applied Energy | Year: 2013
Platinum is the most effective electro-catalyst for oxidation and reduction processes in direct methanol fuel cells (DMFCs). Although platinum and its alloys show desirable electrochemical activities, these catalysts are expensive and make the commercialization of DMFC less attractive. Beside, literature reviews show that tremendous improvements of the activity and stability of non-platinum cathode catalysts have been achieved over the past few years. However, problems including low reaction rates, high over-potentials and low stabilities that remain unsolved particularly for cathode catalyst are discussed in this paper. This paper also describes the various types of non-platinum materials that can potentially substitute for platinum cathode catalysts in DMFC like macrocyclic molecules such as porphyrins and phthalocyanines, transition metal oxides, transition metal sulfides, amorphous transition metal sulfides, and transition metal-based catalysts. Finally, this paper also summarizes the preparation procedure and the performance of various potential cathode catalysts for DMFC operated in acidic and alkaline media as compared with platinum. © 2012 Elsevier Ltd.
Masseran N.,National University of Malaysia
Energy Conversion and Management | Year: 2015
Analyzing the behaviors of wind direction can complement knowledge concerning wind speed and help researchers draw conclusions regarding wind energy potential. Knowledge of the wind's direction enables the wind turbine to be positioned in such a way as to maximize the total amount of captured energy and optimize the wind farm's performance. In this paper, first-order and higher-order Markov chain models are proposed to describe the probabilistic behaviors of wind-direction data. A case study is conducted using data from Mersing, Malaysia. The wind-direction data are classified according to an eight-state Markov chain based on natural geographical directions. The model's parameters are estimated using the maximum likelihood method and the linear programming formulation. Several theoretical arguments regarding the model are also discussed. Finally, limiting probabilities are used to determine a long-run proportion of the wind directions generated. The results explain the dominant direction for Mersing's wind in terms of probability metrics. ©2014 Elsevier Ltd. All rights reserved.
Nadzirin N.,National University of Malaysia
Nucleic acids research | Year: 2013
We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/.