Showing items 41 - 60 of 69

Interacting motif networks located in hotspots associated with RNA release are conserved in Enterovirus capsids

- Ross, Caroline J, Knox, Caroline M, Tastan Bishop, Özlem

  • Authors: Ross, Caroline J , Knox, Caroline M , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/124855 , vital:35704 , https://doi.10.1002/1873-3468.12663
  • Description: Enteroviruses are responsible for a multitude of human diseases. Expansion of the virus capsid is associated with a cascade of conformational changes that allow the subsequent release of RNA. For the first time, this study presents a comprehensive bioinformatic screen for the prediction of interacting motifs within intraprotomer interfaces and across respective interfaces surrounding the fivefold and twofold axes. The results identify a network of conserved motif residues involved in interactions in enteroviruses that may be critical to capsid stabilisation, providing guidelines towards developing antivirals that interfere with viral expansion during RNA release.
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  • Date Issued: 2017

MD-TASK: a software suite for analyzing molecular dynamics trajectories

- Brown, David K, Penkler, David L, Amamuddy, Olivier S, Ross, Caroline J, Atilgan, Ali R, Atilgan, Canan, Tastan Bishop, Özlem

  • Authors: Brown, David K , Penkler, David L , Amamuddy, Olivier S , Ross, Caroline J , Atilgan, Ali R , Atilgan, Canan , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/125138 , vital:35735 , https://doi.10.1093/bioinformatics/btx349
  • Description: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.
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  • Date Issued: 2017

No evidence for association with APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations:

- Kimuda, Magambo Phillip, Noyes, Harry, Mulindwa, Julius, Enyaru, John, Alibu, Vincent Pius, Sidibe, Issa, Mumba, Dieuodonne, Hertz-Fowler, Christiane, MacLeod, Annette, Tastan Bishop, Özlem, Matovu, Enock

  • Authors: Kimuda, Magambo Phillip , Noyes, Harry , Mulindwa, Julius , Enyaru, John , Alibu, Vincent Pius , Sidibe, Issa , Mumba, Dieuodonne , Hertz-Fowler, Christiane , MacLeod, Annette , Tastan Bishop, Özlem , Matovu, Enock
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148272 , vital:38725 , doi: 10.1371/journal.pntd.0006300
  • Description: Human African trypanosomiasis (HAT) manifests as an acute form caused by Trypanosoma brucei rhodesiense (Tbr) and a chronic form caused by Trypanosoma brucei gambiense (Tbg). Previous studies have suggested a host genetic role in infection outcomes, particularly for APOL1. We have undertaken a candidate gene association studies (CGAS) in a Ugandan Tbr and a Tbg HAT endemic area, to determine whether polymorphisms in IL10, IL8, IL4, HLAG, TNFA, TNX4LB, IL6, IFNG, MIF, APOL1, HLAA, IL1B, IL4R, IL12B, IL12R, HP, HPR, and CFH have a role in HAT.
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  • Date Issued: 2017

Perturbation–Response Scanning reveals key residues for Allosteric Control in Hsp70:

- Penkler, David L, Sensoy, Özge, Atilgan, Canan, Tastan Bishop, Özlem

  • Authors: Penkler, David L , Sensoy, Özge , Atilgan, Canan , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148195 , vital:38718 , DOI: 10.1021/acs.jcim.6b00775
  • Description: Hsp70 molecular chaperones play an important role in maintaining cellular homeostasis, and are implicated in a wide array of cellular processes, including protein recovery from aggregates, cross-membrane protein translocation, and protein biogenesis. Hsp70 consists of two domains, a nucleotide binding domain (NBD) and a substrate binding domain (SBD), each of which communicates via an allosteric mechanism such that the protein interconverts between two functional states, an ATP-bound open conformation and an ADP-bound closed conformation. The exact mechanism for interstate conversion is not as yet fully understood. However, the ligand-bound states of the NBD and SBD as well as interactions with cochaperones such as DnaJ and nucleotide exchange factor are thought to play crucial regulatory roles. In this study, we apply the perturbation–response scanning (PRS) method in combination with molecular dynamics simulations as a computational tool for the identification of allosteric hot residues in the large multidomain Hsp70 protein.
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  • Date Issued: 2017

PRIMO: an interactive homology modeling pipeline

- Hatherley, Rowan, Brown, David K, Glenister, Michael, Tastan Bishop, Özlem

  • Authors: Hatherley, Rowan , Brown, David K , Glenister, Michael , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148282 , vital:38726 , doi: 10.1371/journal.pone.0166698
  • Description: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling.
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  • Date Issued: 2017

Role of structural bioinformatics in drug discovery by computational SNP analysis: analyzing variation at the protein level

- Brown, David K, Tastan Bishop, Özlem

  • Authors: Brown, David K , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/125921 , vital:35832 , https://doi.10.1016/j.gheart.2017.01.009
  • Description: With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation. Structure-based drug discovery and design is increasingly incorporating structural bioinformatics techniques to model and analyze protein targets, perform large scale virtual screening to identify hit to lead compounds, and simulate molecular interactions. These techniques are fast, cost-effective, and complement existing experimental techniques such as high throughput sequencing. In this paper, we discuss the contributions of structural bioinformatics to drug discovery, focusing particularly on the analysis of nonsynonymous single nucleotide polymorphisms. We conclude by suggesting a protocol for future analyses of the structural effects of nonsynonymous single nucleotide polymorphisms on proteins and protein complexes.
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  • Date Issued: 2017

Structure-based analysis of single nucleotide variants in the renin-angiotensinogen complex:

- Brown, David K, Olivier, Sheik Amamuddy, Tastan Bishop, Özlem

  • Authors: Brown, David K , Olivier, Sheik Amamuddy , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/147994 , vital:38700 , https://doi.org/10.1016/j.gheart.2017.01.006
  • Description: The renin-angiotensin system (RAS) plays an important role in regulating blood pressure and controlling sodium levels in the blood. Hyperactivity of this system has been linked to numerous conditions including hypertension, kidney disease, and congestive heart failure. Three classes of drugs have been developed to inhibit RAS. In this study, we provide a structure-based analysis of the effect of single nucleotide variants (SNVs) on the interaction between renin and angiotensinogen with the aim of revealing important residues and potentially damaging variants for further inhibitor design purposes.
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  • Date Issued: 2017

The evaluation and validation of copper (II) force field parameters of the Auxiliary Activity family 9 enzymes:

- Moses, Vuyani, Tastan Bishop, Özlem, Lobb, Kevin A

  • Authors: Moses, Vuyani , Tastan Bishop, Özlem , Lobb, Kevin A
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148206 , vital:38719 , DOI: 10.1016/j.cplett.2017.04.022
  • Description: The Auxiliary Activity family 9 (AA9) proteins are Cu2+ coordinating enzymes which are crucial for the early stages of cellulose degradation. In this study, the force field parameters for copper-containing bonds in the Type 1 AA9 protein active site were established and used in a molecular dynamics simulation on a solvated, neutralized system containing an AA9 protein, Cu2+ and a β-cellulose surface. The copper to cellulose interaction was evident during the dynamics, which could also be accelerated by the use of high Cu O van der Waals parameters. The interaction of AA9, Cu2+ and cellulose is described in detail.
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  • Date Issued: 2017

The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype:

- Cornick, Jennifer E, Tastan Bishop, Özlem, Yalcin, Feyruz, Kiran, Anmol M, Kumwenda, Benjamin, Chaguza, Chrispin, Govindpershad, Shanil, Ousmane, Sani, Senghore, Madikay, du Plessis, Mignon, Pluschke, Gerd, 1952-, Ebruke, Chinelo, McGee, Lesley, Sigaùque , Beutel, Collard, Jean-Marc, Bentley, Stephen D, Kadioglu , Aras, Antonio, Martin, von Gottberg, Anne, French, Neil, Klugman, Keith P, Heyderman, Robert S, Alderson, Mark, Everett, Dean B

The role of structural bioinformatics in drug discovery via computational SNP analysis–a proposed protocol for analyzing variation at the protein level:

- Brown, David K, Tastan Bishop, Özlem

  • Authors: Brown, David K , Tastan Bishop, Özlem
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/162914 , vital:40996 , doi: 10.1016/j.gheart.2017.01.009
  • Description: With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps towards an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as Genome-Wide Association Studies (GWAS) and Candidate Gene Association Studies (CGAS). However, these statistical methods do not provide an understanding of the functional effects of variation. Structure-based drug discovery and design is increasingly incorporating structural bioinformatics techniques to model and analyze protein targets, perform large scale virtual screening to identify hit to lead compounds, and simulate molecular interactions. These techniques are fast, cost-effective, and complement existing experimental techniques such as High Throughput Sequencing (HTS).
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  • Date Issued: 2017

Analysis of non-peptidic compounds as potential malarial inhibitors against plasmodial cysteine proteases via integrated virtual screening workflow

- Musyoka, Thommas M, Kanzi, Aquillah M, Lobb, Kevin A, Tastan Bishop, Özlem

  • Authors: Musyoka, Thommas M , Kanzi, Aquillah M , Lobb, Kevin A , Tastan Bishop, Özlem
  • Date: 2016
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/123074 , vital:35403 , https://doi.10.1080/07391102.2015.1108231
  • Description: Malaria is an infectious disease caused by a diverse group of erythrocytic protozoan parasites of the genus Plasmodium. It remains an exigent public health problem in the tropical areas of Africa, South America and parts of Asia and continues to take its toll in morbidity and mortality with half of the world’s population under a permanent risk of infection leading to more than half a million deaths annually (WHO, 2013). Five Plasmodium species, namely P. falciparum (Pf ), P. vivax (Pv), P. ovale (Po), P. malariae (Pm) and P. knowlesi (Pk), are known to infect humans with Pf responsible for more than 90% of the malarial fatalities reported in sub-Saharan Africa. The predominance of Pf is attributed to its adaptability (Ashley, McGready, Proux, & Nosten, 2006; Prugnolle et al., 2011). Although the high occurrence of the Duffy negative trait among African populations lowers the threat posed by Pv, it is the most frequent and widely causative agent of benign tertian malaria in other parts of the world (Mendis, Sina, Marchesini, & Carter, 2001). In addition to the listed human malarial parasite forms, several other Plasmodium species, which infect non-human laboratory models, have been identified and are of significant importance in understanding the parasite biology, the host–parasite interactions and in the drug development process (Langhorne et al., 2011).
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  • Date Issued: 2016

Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins:

- Moses, Vuyani, Hatherley, Rowan, Tastan Bishop, Özlem

  • Authors: Moses, Vuyani , Hatherley, Rowan , Tastan Bishop, Özlem
  • Date: 2016
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148358 , vital:38732 , DOI: 10.1186/s13068-016-0655-2
  • Description: Due to the impending depletion of fossil fuels, it has become important to identify alternative energy sources. The biofuel industry has proven to be a promising alternative. However, owing to the complex nature of plant biomass, hence the degradation, biofuel production remains a challenge. The copper-dependent Auxiliary Activity family 9 (AA9) proteins have been found to act synergistically with other cellulose-degrading enzymes resulting in an increased rate of cellulose breakdown. AA9 proteins are lytic polysaccharide monooxygenase (LPMO) enzymes, otherwise known as polysaccharide monooxygenases (PMOs). They are further classified as Type 1, 2 or 3 PMOs, depending on the different cleavage products formed. As AA9 proteins are known to exhibit low sequence conservation, the analysis of unique features of AA9 domains of these enzymes should provide insights for the better understanding of how different AA9 PMO types function.
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  • Date Issued: 2016

Structure based docking and molecular dynamic studies of plasmodial cysteine proteases against a South African natural compound and its analogs:

- Musyoka, Thommas M, Kanzi, Aquillah M, Lobb, Kevin A, Tastan Bishop, Özlem

  • Authors: Musyoka, Thommas M , Kanzi, Aquillah M , Lobb, Kevin A , Tastan Bishop, Özlem
  • Date: 2016
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148027 , vital:38703 , DOI: 10.1038/srep23690
  • Description: Identification of potential drug targets as well as development of novel antimalarial chemotherapies with unique mode of actions due to drug resistance by Plasmodium parasites are inevitable. Falcipains (falcipain-2 and falcipain-3) of Plasmodium falciparum, which catalyse the haemoglobin degradation process, are validated drug targets. Previous attempts to develop peptide based drugs against these enzymes have been futile due to the poor pharmacological profiles and susceptibility to degradation by host enzymes. This study aimed to identify potential non-peptide inhibitors against falcipains and their homologs from other Plasmodium species.
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  • Date Issued: 2016

Subcellular localisation of Theiler's murine encephalomyelitis virus (TMEV) capsid subunit VP1 vis-á-vis host protein Hsp90:

- Ross, Caroline J, Upfold, Nicole, Luke, Garry A, Tastan Bishop, Özlem, Knox, Caroline M

  • Authors: Ross, Caroline J , Upfold, Nicole , Luke, Garry A , Tastan Bishop, Özlem , Knox, Caroline M
  • Date: 2016
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148016 , vital:38702 , DOI: 10.1016/j.virusres.2016.06.003
  • Description: The VP1 subunit of the picornavirus capsid is the major antigenic determinant and mediates host cell attachment and virus entry. To investigate the localisation of Theiler's murine encephalomyelitis virus (TMEV) VP1 during infection, a bioinformatics approach was used to predict a surface-exposed, linear epitope region of the protein for subsequent expression and purification. This region, comprising the N-terminal 112 amino acids of the protein, was then used for rabbit immunisation, and the resultant polyclonal antibodies were able to recognise full length VP1 in infected cell lysates by Western blot. Following optimisation, the antibodies were used to investigate the localisation of VP1 in relation to Hsp90 in infected cells by indirect immunofluorescence and confocal microscopy.
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  • Date Issued: 2016

The development of computational biology in South Africa: successes achieved and lessons learnt

- Mulder, Nicola J, Christoffels, Alan, De Oliveira, Tulio, Gamieldien, Junaid, Hazelhurst, Scott, Joubert, Fourie, Kumuthini, Judit, Pillay, Ché S, Snoep, Jacky L, Tastan Bishop, Özlem, Tiffin, Nicki

  • Authors: Mulder, Nicola J , Christoffels, Alan , De Oliveira, Tulio , Gamieldien, Junaid , Hazelhurst, Scott , Joubert, Fourie , Kumuthini, Judit , Pillay, Ché S , Snoep, Jacky L , Tastan Bishop, Özlem , Tiffin, Nicki
  • Date: 2016
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148347 , vital:38731 , DOI: 10.1371/journal.pcbi.1004395
  • Description: Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
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  • Date Issued: 2016

Human, vector and parasite Hsp90 proteins: a comparative bioinformatics analysis

- Faya, Ngonidzashe, Penkler, David L, Tastan Bishop, Özlem

  • Authors: Faya, Ngonidzashe , Penkler, David L , Tastan Bishop, Özlem
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148038 , vital:38704 , DOI: 10.1016/j.fob.2015.11.003
  • Description: The treatment of protozoan parasitic diseases is challenging, and thus identification and analysis of new drug targets is important. Parasites survive within host organisms, and some need intermediate hosts to complete their life cycle. Changing host environment puts stress on parasites, and often adaptation is accompanied by the expression of large amounts of heat shock proteins (Hsps). Among Hsps, Hsp90 proteins play an important role in stress environments. Yet, there has been little computational research on Hsp90 proteins to analyze them comparatively as potential parasitic drug targets. Here, an attempt was made to gain detailed insights into the differences between host, vector and parasitic Hsp90 proteins by large-scale bioinformatics analysis.
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  • Date Issued: 2015

JMS: a workflow management system and web-based cluster front-end for the Torque resource manager

- Brown, David K, Musyoka, Thommas M, Penkler, David L, Tastan Bishop, Özlem

  • Authors: Brown, David K , Musyoka, Thommas M , Penkler, David L , Tastan Bishop, Özlem
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148049 , vital:38705 , https://arxiv.org/abs/1501.06907
  • Description: Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over distributed computer clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing.
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  • Date Issued: 2015

JMS: an open source workflow management system and web-based cluster front-end for high performance computing

- Brown, David K, Penkler, David L, Musyoka, Thommas M, Tastan Bishop, Özlem

  • Authors: Brown, David K , Penkler, David L , Musyoka, Thommas M , Tastan Bishop, Özlem
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/162880 , vital:40993 , doi:10.1371/journal.pone.0134273
  • Description: Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality.
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  • Date Issued: 2015

Plasmodium falciparum Hop: detailed analysis on complex formation with Hsp70 and Hsp90

- Hatherley, Rowan, Clitheroe, Crystal-Leigh, Faya, Ngonidzashe, Tastan Bishop, Özlem

  • Authors: Hatherley, Rowan , Clitheroe, Crystal-Leigh , Faya, Ngonidzashe , Tastan Bishop, Özlem
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/125708 , vital:35810 , https://doi.10.1016/j.bbrc.2014.11.103
  • Description: The heat shock organizing protein (Hop) is important in modulating the activity and co-interaction of two chaperones: heat shock protein 70 and 90 (Hsp70 and Hsp90). Recent research suggested that Plasmodium falciparum Hop (PfHop), PfHsp70 and PfHsp90 form a complex in the trophozoite infective stage. However, there has been little computational research on the malarial Hop protein in complex with other malarial Hsps. Using in silico characterization of the protein, this work showed that individual domains of Hop are evolving at different rates within the protein. Differences between human Hop (HsHop) and PfHop were identified by motif analysis. Homology modeling of PfHop and HsHop in complex with their own cytosolic Hsp90 and Hsp70 C-terminal peptide partners indicated excellent conservation of the Hop concave TPR sites bound to the C-terminal motifs of partner proteins. Further, we analyzed additional binding sites between Hop and Hsp90, and showed, for the first time, that they are distinctly less conserved between human and malaria parasite. These sites are located on the convex surface of Hop TPR2, and involved in interactions with the Hsp90 middle domain. Since the convex sites are less conserved than the concave sites, it makes their potential for malarial inhibitor design extremely attractive (as opposed to the concave sites which have been the focus of previous efforts).
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  • Date Issued: 2015

SANCDB: a South African natural compound database

- Hatherley, Rowan, Brown, David K, Musyoka, Thommas M, Penkler, David L, Faya, Ngonidzashe, Lobb, Kevin A, Tastan Bishop, Özlem

  • Authors: Hatherley, Rowan , Brown, David K , Musyoka, Thommas M , Penkler, David L , Faya, Ngonidzashe , Lobb, Kevin A , Tastan Bishop, Özlem
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148337 , vital:38730 , DOI: 10.1186/s13321-015-0080-8
  • Description: Natural products (NPs) are important to the drug discovery process. NP research efforts are expanding world-wide and South Africa is no exception to this. While freely-accessible small molecule databases, containing compounds isolated from indigenous sources, have been established in a number of other countries, there is currently no such online database in South Africa.
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  • Date Issued: 2015
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