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A rational free energy-based approach to understanding and targeting disease-causing missense mutations

Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov
2013 JAMIA Journal of the American Medical Informatics Association  
The 3D structures were used to predict the effect of disease-causing missense mutations on the folding free energy, conformational dynamics, hydrogen bond network and, if appropriate, protein-protein binding  ...  free energy.  ...  Funding The work of ZZ and EA was supported in part by NIH, NLM, grant number 1R03LM009748.  ... 
doi:10.1136/amiajnl-2012-001505 pmid:23408511 pmcid:PMC3721167 fatcat:5mih3em4pvbtnjfash6wyugdzy

Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery

Nagasundaram Nagarajan, Edward K. Y. Yapp, Nguyen Quoc Khanh Le, Balu Kamaraj, Abeer Mohammed Al-Subaie, Hui-Yuan Yeh
2019 BioMed Research International  
The goal is to exploit modern computational biology and machine learning systems to predict the molecular behaviour and the likelihood of getting a useful drug, thus saving time and money on unnecessary  ...  Artificial intelligence (AI) proves to have enormous potential in many areas of healthcare including research and chemical discoveries.  ...  Acknowledgments e authors take this opportunity to thank the Nanyang Technological University for providing the facilities and for encouragement to carry out this work.  ... 
doi:10.1155/2019/8427042 pmid:31886259 pmcid:PMC6925679 fatcat:k2fm2n7pfnf63emhkap7arlg4m

RE(ACT)® International Congress on Research on Rare and Orphan Diseases

2011 Molecular Syndromology  
public that many researchers based all around the world are now dedicating their time and efforts to better understand a particular rare disease.  ...  The congress goals are to promote research on rare and orphan diseases among the general public, industry and policy makers, and to bring together researchers and their knowledge to help support the understanding  ...  The effects of the disease-causing mutation in lamin are unlike the effects of lamin deletion, and therefore show that this EDMD-linked mutation acts in a dominant fashion to provoke muscle-specific defects  ... 
doi:10.1159/000336858 fatcat:q67z2gzqzvclvfy7p5gquzvnoa

RE(ACT)®: INTERNATIONAL CONGRESS ON RESEARCH ON RARE AND ORPHAN DISEASES

2012 Molecular Syndromology  
public that many researchers based all around the world are now dedicating their time and efforts to better understand a particular rare disease.  ...  The congress goals are to promote research on rare and orphan diseases among the general public, industry and policy makers, and to bring together researchers and their knowledge to help support the understanding  ...  The effects of the disease-causing mutation in lamin are unlike the effects of lamin deletion, and therefore show that this EDMD-linked mutation acts in a dominant fashion to provoke muscle-specific defects  ... 
pmid:22670144 pmcid:PMC3362213 fatcat:7x4vqttaxrhvjig37e56vknyre

Disease Pathways and Novel Therapeutic Targets in Hypertrophic Cardiomyopathy

H. Ashrafian, W. J. McKenna, H. Watkins
2011 Circulation Research  
Ashrafian reports holding a European method-of-use patent for perhexiline in systolic heart failure and having patents pending for its use in diastolic heart failure and hypertrophic cardiomyopathy and  ...  Not only does this study support the hypothesis that energy deficiency causatively contributes to HCM, but it provides a rationale for the application of metabolic therapies in HCM.  ...  organ physiology 17 are rational therapeutic targets.  ... 
doi:10.1161/circresaha.111.242974 pmid:21700950 fatcat:snbarxqsgzgidl6qlunqfg4qky

Molecular modelling and simulations in cancer research

Ran Friedman, Kjetil Boye, Kjersti Flatmark
2013 Biochimica et Biophysica Acta. CR. Reviews on Cancer  
of a protein bound to a drug molecule is known, and you want to 101 understand whether a certain mutation may lead to drug resistance because it would reduce the affinity 102 of the drug molecule. 103  ...  In 111 practice, the potential energy of the system is estimated based on a set of equations and parameters, 112 collectively known as a force field.  ...  and A.10, 365 where we list several applications, commercial as well as free.  ... 
doi:10.1016/j.bbcan.2013.02.001 pmid:23416097 fatcat:6wyfplnxdzdpdhhbf25ln7itry

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Vaishali P Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J Wodak, Vincent Zoete, Sameer Velankar, Christine Orengo
2020 Briefings in Bioinformatics  
SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective treatment is currently available to combat the disease.  ...  We also discuss the impact of these resources and structure-based studies, to understand various aspects of SARS-CoV-2 infection and therapeutic development.  ...  to cause severe disease in humans.  ... 
doi:10.1093/bib/bbaa362 pmid:33348379 fatcat:24w5gfkifrc35ohdcpl5chmpka

Computational Approaches to Prioritize Cancer Driver Missense Mutations

Feiyang Zhao, Lei Zheng, Alexander Goncearenco, Anna Panchenko, Minghui Li
2018 International Journal of Molecular Sciences  
Effects caused by missense mutations can be pinpointed by in silico modeling, which makes it more feasible to find a treatment and reverse the effect.  ...  Missense mutations, which can render proteins non-functional and provide a selective growth advantage to cancer cells, are frequently detected in cancer.  ...  MutaBind is a web-based application method for evaluation of the effects of sequence variants and disease mutations on protein-protein interactions [48] .  ... 
doi:10.3390/ijms19072113 pmid:30037003 pmcid:PMC6073793 fatcat:vjhbg455ubappidap7lqo7y3za

In silico investigation of functional nsSNPs – an approach to rational drug design

Arantxa Rodriguez-Casado
2012 Research and Reports in Medicinal Chemistry  
Additionally, the review details the recent advances in the field of in silico pharmacogenomics, which provide insight into disease phenotypes and individual susceptibility to disease.  ...  It also explains current methods by which to predict the functional impact of nsSNPs based on physicochemical amino acid properties, sequence information, and structural attributes.  ...  Acknowledgments This work has been supported by the Spanish Ministry of Science and Innovation (R&C2007-01920).  ... 
doi:10.2147/rrmc.s28211 fatcat:fmghecofqfg6dbw2wlz4wekh2m

Genetically-engineered hamster models: applications and perspective in dyslipidemia and atherosclerosis-related cardiovascular disease

George Liu, Pingping Lai, Jiabao Guo, Yuhui Wang, Xunde Xian
2021 Medical Review  
However, based on the concept of precision medicine and high demand of translational research, the applications of mouse models for human ASCVD study would be limited due to the natural differences in  ...  suggesting that gene-targeted hamster models will provide new insights into the precision medicine and translational research of ASCVD.  ...  a platform to develop therapeutic approaches to low HDL and ASCVD caused by FLD.  ... 
doi:10.1515/mr-2021-0004 fatcat:j7mpjwzelbhorgukeobxtim7c4

Emerging trends at the interface of chemistry and biology: Applications to the design of human therapeutics

Santanu Bhattacharya, Raghavan Varadarajan
2010 Proceedings of the Indian Academy of sciences. Chemical sciences  
Advances in protein design methodology and screening are described, with a focus on their application to the design of antibody based therapeutics.  ...  Strategies for multi-target therapeutics and network analysis with a focus on cancer and HIV are discussed.  ...  R V thanks Bharat Adkar and Piyali Saha for providing figures and Bhagyashree K G for help with manuscript preparation.  ... 
doi:10.1007/s12039-010-0034-7 fatcat:cu5bghpverfa7lyoayg44rw32e

Abstracts of the 12th UK Neuromuscular Translational Research Conference, 4th and 5th April 20191

Volker Straub
2019 Journal of Neuromuscular Diseases  
team to produce the highest professional level of neuromuscular clinical research in Newcastle and the North East.  ...  OD17 Immune-array genotyping association analysis in a large cohort of sporadic inclusion body myositis and controls  ...  The suggested grouping intended to be a rational approach to RD ERN planning and to ensure coverage of all RD. The work to establish EURO-NMD started in 2013 under Kate Bushby's lead.  ... 
doi:10.3233/jnd-190000 fatcat:s6ovvrwyevaznmdlwuajqimy2q

Abstracts for the 36th Human Genetics Society of Australasia Annual Scientific Meeting Canberra, Australia July 22–25, 2012

2012 Twin Research and Human Genetics  
disease models.  ...  , a musclespecific COX15 knockout, and a Sco2 knockout/knockin (KO/KI) mouse.  ...  AACG Oral 10 MUTATIONS IN EXONS 41 AND 42 OF FIBRILLIN 1 CAUSE SHORT STATURE OF THE ACROMELIC TYPE.  ... 
doi:10.1017/thg.2012.44 fatcat:6wam3e3zgvhabfxbseysnomuki

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Yunhui Peng, Emil Alexov, Sankar Basu
2019 International Journal of Molecular Sciences  
However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious.  ...  parameters, namely, folding and binding free energies potentially serve as effective biomarkers.  ...  Several computational approaches have been developed to predict folding and binding free energy changes (∆∆G) as a mean to link them with pathogenicity of mutations.  ... 
doi:10.3390/ijms20030548 fatcat:f257huiwz5gdvgtur7pq4aydl4

Antibodies targeting enzyme inhibition as potential tools for research and drug development

José Manuel Pérez de la Lastra, Victoria Baca-González, Sergio González-Acosta, Patricia Asensio-Calavia, Andrea Otazo-Pérez, Antonio Morales-delaNuez
2021 Biomolecular Concepts  
Antibodies have transformed biomedical research and are now being used for different experimental applications.  ...  Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity.  ...  With no clinical data to support or refute the amyloid theory, new approaches to addressing potential targets are required.  ... 
doi:10.1515/bmc-2021-0021 pmid:35104929 fatcat:a2tiieulqvemvhpg7ccq725agy
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