Application of Non-uniform Sampling to Three Dimensional Carbon Direct-detection NMR Experiment

지준구 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.10

Systematic Assessment of the Effects of an All-Atom Force Field and the Implicit Solvent Model on the Refinement of NMR Structures with Subsets of Distance Restraints

지준구 대한화학회 2014 Bulletin of the Korean Chemical Society Vol.35 No.7

Employment of a time consuming, sophisticated calculation using the all-atom force field and generalized- Born implicit solvent model (GBIS) for refinement of NMR structures has become practical through advances in computational methods and capacities. GBIS refinement improves the qualities of the resulting NMR structures with reduced computational times. However, the contribution of GBIS to NMR structures has not been sufficiently studied in a quantitative way. In this paper, we report the effects of GBIS on the refined NMR structures of ubiquitin (UBQ) and GB1 with subsets of distance restraints derived from experimental data. Random omission prepared a series of distance restraints 0.05, 0.1, 0.3, 0.5, and 0.7 times smaller. For each number, we produced five different restraints for statistical analysis. We then recalculated the NMR structures using CYANA software, followed by GBIS refinements using the AMBER package. GBIS improved both the precision and accuracy of all the structures, but to varied levels. The degrees of improvement were significant when the input restraints were insufficient. In particular, GBIS enabled GB1 to form an accurate structure even with distance restraints of 5%, revealing that the root-mean-square deviation was less than 1 Å from the X-ray backbone structure. We also showed that the efficiency of searching the conformational space was more important for finding accurate structures with the calculation of UBQ with 5% distance restraints than the number of conformations generated. Our data will provide a meaningful guideline to judge and compare the structural improvements by GBIS.

Refinement of protein NMR structures using atomistic force field and implicit solvent model: Comparison of the accuracies of NMR structures with Rosetta refinement

지준구 한국자기공명학회 2022 Journal of the Korean Magnetic Resonance Society Vol.26 No.1

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer—even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

Letter to Editor: Accelerating atomistic refinement of NMR structures using Graphics Processing Unit

지준구 한국자기공명학회 2014 Journal of the Korean Magnetic Resonance Society Vol.18 No.2

we showed a dramatic acceleration of GBIS calculations by using GPU, which almost compensates the longer computational times required for GBIS. To the best of our knowledge, this is the first report of using GPU for refining the NMR structures. The 1500 ps calculation for 100 structures would be one of the longest atomistic refinements. This approach would permit a wider use of GBIS, even on moderately expensive hardware. GPU-accelerated GBIS could be particularly useful for biomolecules whose structures are difficult to determine by conventional NMR methods, such as membrane proteins and protein–protein complexes. It is difficult to obtain sufficient experimental restraints in the cases. The calculations with HN-HN restraints may approximate the situations. In this study, rSA was used for searching conformational space. One can combine sophisticated algorithm such as replica exchange17 with GPU instead. Our results will be a meaningful guideline in applying GPU-based acceleration into calculating NMR structure.

Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

지준구 대한화학회 2010 Bulletin of the Korean Chemical Society Vol.31 No.9

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Comparison of NMR structures refined under implicit and explicit solvents

지준구 한국자기공명학회 2015 Journal of the Korean Magnetic Resonance Society Vol.19 No.1

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

Effects of force fields for refining protein NMR structureswith atomistic force fields and generalized-Born implicit solvent model

지준구 한국자기공명학회 2014 Journal of the Korean Magnetic Resonance Society Vol.18 No.1

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields¾ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13¾with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

Strategy for Determining the Structures of Large Biomolecules using the Torsion Angle Dynamics of CYANA

지준구 한국자기공명학회 2016 Journal of the Korean Magnetic Resonance Society Vol.20 No.4

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1‒70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

Effects of generalized-Born implicit solvent models in NMR structure refinement

지준구 한국자기공명학회 2013 Journal of the Korean Magnetic Resonance Society Vol.17 No.1

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

UGV(Unmanned Ground Vehicle) 플랫폼의 작업 영역 경로 추종에 관한 연구

지준구 ( Jun-goo Ji ),이명규 ( Myung-gyu Lee ),김종탁 ( Jong-tak Kim ),김원균 ( Won-gyun Kim ),최준원 ( Jun-won Choi ) 한국농업기계학회 2023 한국농업기계학회 학술발표논문집 Vol.28 No.2

양돈업계는 종래의 소규모 양돈 환경에서 대규모 양돈 환경으로 기업화 및 규격화를 도모하고 있다. 이에 양돈 축사내 자동화 시설의 도입이 증가하고 있으며, 농촌 지역의 고질적인 인력 감소, 고령화 현상에 대비하고 있다. 특히 양돈농가의 자동화는 자율작업이 가능한 로봇을 적용하려는 연구가 활발히 진행되고 있으며, 이를 위한 돈사 규격 맞춤형 실내 자율주행 알고리즘의 개발이 필요한 실정이다. 본 논문에서는 자율주행 무인 돈사 관리 플랫폼의 주행 환경 및 성능에 기반하여, 무인 돈사 환경 내부를 주행하면서 강력한 수압을 가진 물줄기를 분사하여 바닥 면의 분뇨 및 오염물을 효과적으로 제거하기 위한 경로 추종 제어 알고리즘 개발하였다. 개발한 제어 알고리즘의 성능 평가를 위해, 실제 돈사 환경과 유사한 환경을 설치하였으며 주행 경로의 경우 실제 환경을 기반으로 경로를 생성하였다. 제어 알고리즘은 Stanley Method, Pure Pursuit 그리고 Feed Forward를 추가한 modified Stanley Method 알고리즘을 개발하여 돈사 환경에 적용하였으며 그 성능을 비교하여 평가하였다. 실제 실험 결과, modified Stanley Method 알고리즘의 평균 주행 오차가 0.03m로 기존 모델의 추종 결과보다 우수하며, 돈사 환경에 적합한 것을 확인하였다. 아울러 규격화된 돈사 환경에 우수한 적합성을 보임에 따라 향후 현대식 양돈업계 전반에 돈사 로봇 플랫폼의 자율주행 알고리즘으로 충분히 활용될 것으로 판단된다.