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Folding Very Short Peptides Using Molecular Dynamics

Bosco K. Ho, Ken A. Dill
2006 PLoS Computational Biology  
Citation: Ho BK, Dill KA (2006) Folding very short peptides using molecular dynamics. PLoS Comput Biol 2(4): e27.  ...  From the distribution of X k E , we calculate a new estimate of f k by X k E ¼ N k E N k expðf k À b k EÞ ð1Þ f k ¼ Àlog X E X k E expðb k EÞ " # ð2Þ We iterate the above two steps until f k converges.  ...  Starting with a crude estimate of f k , we calculate X k E -the weight of states with energy E in replica k: where N k E is the number of snapshots in replica k with energy E.  ... 
doi:10.1371/journal.pcbi.0020027 pmid:16617376 pmcid:PMC1435986 fatcat:r767xr5ngndzxkc3eaf2n7kzzm

The Ramachandran plots of glycine and pre-proline

Bosco K Ho, Robert Brasseur
2005 BMC Structural Biology  
We carried out a re-evaluation of the steric map of glycine ( Figure 2B ) by following the methodology of Ho and coworkers [3] .  ... 
doi:10.1186/1472-6807-5-14 pmid:16105172 pmcid:PMC1201153 fatcat:enicdbji7vhenf5hajvwt3qvxe

Correction: Folding Very Short Peptides Using Molecular Dynamics

Bosco K. Ho, Ken A. Dill
2006 PLoS Computational Biology  
Citation: (2005) Correction: Folding very short peptides using molecular dynamics. PLoS Comput Biol 2(5): e60.
doi:10.1371/journal.pcbi.0020060 fatcat:aipqs6dimfdrjnejmun3ibzpfm

Hybrid approaches to molecular simulation

Bosco K Ho, David Perahia, Ashley M Buckle
2012 Current Opinion in Structural Biology  
In ATD, the PDZ protein is cooled down to 10 K, then, after position constraints are applied to the backbone and surface atoms, a temperature couple is applied to a single residue.  ...  This is a noisy graph that has been the basis of many studies of the allostery of the PDZ domain. 16 . 16 Sharp K, Skinner JJ: Pump-probe molecular dynamics as a tool for studying protein motion and  ... 
doi:10.1016/j.sbi.2012.05.005 pmid:22633678 fatcat:yv46byl7mnhgzpcgk3qdlgybei

Interactive visualization tools for the structural biologist

Benjamin T. Porebski, Bosco K. Ho, Ashley M. Buckle
2013 Journal of Applied Crystallography  
General comments and suggestions for improvements are welcome and should be addressed to Ashley Buckle at ashley.buckle@monash. edu or Bosco Ho at bosco.ho@monash.edu.  ...  Figure 3 3 Figure 3 , Ho and Buckle Interactive visualization tools J. Appl. Cryst. (2013). 46, 1518-1520 Figure 4 4 Figure 4  ... 
doi:10.1107/s0021889813017858 pmid:24068844 pmcid:PMC3778324 fatcat:p5mpdqaaxvfobn7cbypyaae2nm

Twist and shear in β-sheets and β-ribbons

Bosco K. Ho, Paul M.G. Curmi
2002 Journal of Molecular Biology  
Parallel wide residue in: (i) b-sheet, slope À0.22, corr À0.27; (j) b-ribbon, slope À0.25, corr À0.27; (k) model; and (l) reduced model.  ...  The resulting region of the Ramachandran plot is (À150 < f < À90 ; 116 < c < 150 ), which is asymmetric with respect to the diagonal ( Figure 5 (c) and (k)).  ...  the values of c > 116 correlate to d(O Á Á ÁC b ) > 2.9 A Ê in all b-ribbon residues ( Figure 6 of the main text: (i) antiparallel non-H-bonded pair residue; (j) antiparallel Hbonded pair residue; (k)  ... 
doi:10.1006/jmbi.2001.5385 pmid:11902844 fatcat:fiyqaavlfvfaljteilipfsgs6i

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Bosco K. Ho, David A. Agard, Michael Levitt
2009 PLoS Computational Biology  
Because of the reduced degrees of freedom, imposing a sidechain rotamer kinetic energy of 300 K results in far greater rotational velocities than those in a standard 300 K MD simulation.  ...  In the graph, the Y-axis standard velocities (extracted from standard molecular-dynamics at 300 K) are plotted against the X-axis RIP velocities (in the RIP protocol the kinetic energy at 300 K are effectively  ... 
doi:10.1371/journal.pcbi.1000343 pmid:19343225 pmcid:PMC2660149 fatcat:k434s4qejjbt5kogrycfd7sf4u

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

Andrew J Perry, Bosco K Ho
2013 Source Code for Biology and Medicine  
The annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving experiments can indicate exposed regions of membrane proteins that may contain antigenic determinants or constitute vaccine targets in pathogenic bacteria. Results: Inmembrane is a tool to predict the membrane proteins with surface-exposed regions of polypeptide in sets of bacterial protein
more » ... sequences. We have re-implemented a protocol for Gram-positive bacterial proteomes, and developed a new protocol for Gram-negative bacteria, which interface with multiple predictors of subcellular localization and membrane protein topology. Through the use of a modern scripting language, inmembrane provides an accessible code-base and extensible architecture that is amenable to modification for related sequence annotation tasks. Conclusions: Inmembrane easily integrates predictions from both local binaries and web-based queries to help gain an overview of likely surface exposed protein in a bacterial proteome. The program is hosted on the Github repository http://github.com/boscoh/inmembrane.
doi:10.1186/1751-0473-8-9 pmid:23506117 pmcid:PMC3668253 fatcat:5irveoi6v5dnbc4lcvkqjpy6va

Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix

Bosco K. Ho, Annick Thomas, Robert Brasseur
2009 Protein Science  
Ho and Curmi (2002) showed that restrictions due to hydrogen bonds in ␤-sheet formation induce a diagonal ␤-strand region.  ...  For example, Ho and Curmi (2002) showed that in the allowed regions of in ␤-sheet residues, there is an O i−1 ···H ␣ nonbonded electrostatic interaction where most of the observed values are found below  ... 
doi:10.1110/ps.03235203 pmid:14573863 pmcid:PMC2366959 fatcat:mtcwzxcdrnf6jpwfbkwpagjcqm

Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

Bosco K Ho, David A Agard
2008 BMC Structural Biology  
Identification of new, well-populated amino-acid sidechain rotamers involving hydroxylhydrogen atoms and sulfhydryl-hydrogen atoms. Permalink https://escholarship.org/uc/item/78h8m18c Journal BMC structural biology, 8(1) Abstract Background: An important element in homology modeling is the use of rotamers to parameterize the sidechain conformation. Despite the many libraries of sidechain rotamers that have been developed, a number of rotamers have been overlooked, due to the fact that they
more » ... ve hydrogen atoms. Results: We identify new, well-populated rotamers that involve the hydroxyl-hydrogen atoms of Ser, Thr and Tyr, and the sulfhydryl-hydrogen atom of Cys, using high-resolution crystal structures (<1.2 Å). Although there were refinement artifacts in these structures, comparison with the electron-density maps allowed the placement of hydrogen atoms involved in hydrogen bonds. The χ2 rotamers in Ser, Thr and Cys are consistent with tetrahedral bonding, while the χ3 rotamers in Tyr are consistent with trigonal-planar bonding. Similar rotamers are found in hydrogen atoms that were computationally placed with the Reduce program from the Richardson lab. Conclusion: Knowledge of these new rotamers will improve the evaluation of hydrogen-bonding networks in protein structures.
doi:10.1186/1472-6807-8-41 pmid:19014592 pmcid:PMC2603037 fatcat:jmutezbybbbfvjngwqhrq6bq2m

Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility

Bosco K. Ho, David A. Agard
2010 Protein Science  
K.  ...  Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57:433-443. 32.  ... 
doi:10.1002/pro.318 pmid:20052683 pmcid:PMC2866267 fatcat:k5zdqm2tuvc45olzezts34znh4

An Improved Strategy for Generating Forces in Steered Molecular Dynamics: The Mechanical Unfolding of Titin, e2lip3 and Ubiquitin

Bosco K. Ho, David A. Agard, Anna Kristina Croft
2010 PLoS ONE  
The proteins were pre-equilibrated to 300 K for 100 ps using a Langevin thermometer with a friction coefficient of c = 5 s 21 .  ...  The velocities in the system are first scaled to 300 K. Then modified velocities are generated and applied to the system. The new system are written to new restart files.  ... 
doi:10.1371/journal.pone.0013068 pmid:20927369 pmcid:PMC2947501 fatcat:gazofxabencmtiutzbtckzj2kq

SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms

Seán I O'Donoghue, Andrea Schafferhans, Neblina Sikta, Christian Stolte, Sandeep Kaur, Bosco K Ho, Stuart Anderson, James B Procter, Christian Dallago, Nicola Bordin, Matt Adcock, Burkhard Rost
2021 Molecular Systems Biology  
Function t n e m n g i l A NSP13 Mimicry of Host Proteins B 854 A NSP3 Mimicry of Host Proteins H s o t r P e t o n i N 3 P S A m n g i l e t n D m o a n i y g o l o p o T t o P e t n l l a i y H a j i c k  ... 
doi:10.15252/msb.202010079 pmid:34519429 fatcat:swflm5kc2rfwbffbomvbfub2uq

Listeria monocytogenes Peritonitis in a Patient Receiving Continuous Ambulatory Peritoneal Dialysis: A Case Report and Review of the Literature

Ho-Kwan Sin, Au Cheuk, William Lee, Ka-Fai Yim, Clara Poon, Ivy Wong, Bosco Lam, Hon-Lok Tang, Samuel K. Fung, Yoshihide Fujigaki
2021 Case Reports in Nephrology  
Listeria monocytogenes is a rare cause of peritoneal dialysis-related peritonitis. Only a handful of cases have been reported, and the optimal management is still uncertain. We present a case of Listeria monocytogenes peritonitis and perform a review of the literature to elucidate optimal antibiotic therapy.
doi:10.1155/2021/6681629 pmid:33575047 pmcid:PMC7861955 fatcat:7ojghr24uvaubhfb6l6lwsgahm

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

Phillip Pymm, Patricia T Illing, Sri H Ramarathinam, Geraldine M O'Connor, Victoria A Hughes, Corinne Hitchen, David A Price, Bosco K Ho, Daniel W McVicar, Andrew G Brooks, Anthony W Purcell, Jamie Rossjohn (+1 others)
2017 Nature Structural & Molecular Biology  
HLA-B*57:01 binary and ternary complexes with KIR3DL1*001 were concentrated to ~ 10 mg/mL and crystallized at 294 K by the hanging-drop vapour-diffusion method.  ...  Whilst the global HLA-B*57:01 9-11 amino acid peptide motif shows enrichment of K/I/R at P1, it was observed that N-terminally extended peptides were enriched for S/T/A at P1 and P-1.  ... 
doi:10.1038/nsmb.3381 pmid:28218747 fatcat:rki6v6xtpng3jedgzxr3t6l5da
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