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Folding Very Short Peptides Using Molecular Dynamics
2006
PLoS Computational Biology
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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
2005
BMC Structural Biology
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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
2006
PLoS Computational Biology
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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
2012
Current Opinion in Structural Biology
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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
2013
Journal of Applied Crystallography
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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
2002
Journal of Molecular Biology
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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
2009
PLoS Computational Biology
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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
2013
Source Code for Biology and Medicine
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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
doi:10.1186/1751-0473-8-9
pmid:23506117
pmcid:PMC3668253
fatcat:5irveoi6v5dnbc4lcvkqjpy6va
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... 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.
Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix
2009
Protein Science
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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
2008
BMC Structural Biology
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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
doi:10.1186/1472-6807-8-41
pmid:19014592
pmcid:PMC2603037
fatcat:jmutezbybbbfvjngwqhrq6bq2m
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... 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.
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility
2010
Protein Science
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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
2010
PLoS ONE
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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
2021
Molecular Systems Biology
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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
2021
Case Reports in Nephrology
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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
2017
Nature Structural & Molecular Biology
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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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