A5063144451- Protein Structure and Dynamics
- Robotic Mechanisms and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Robot Manipulation and Learning
- Crystallography and molecular interactions
- Soft Robotics and Applications
- Genomics and Phylogenetic Studies
- Robotic Path Planning Algorithms
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Advanced Numerical Analysis Techniques
- Genome Rearrangement Algorithms
- Glycosylation and Glycoproteins Research
- Manufacturing Process and Optimization
- Algorithms and Data Compression
- Dynamics and Control of Mechanical Systems
- Optimization and Packing Problems
- Optimization and Search Problems
- Computational Geometry and Mesh Generation
- Advanced Electron Microscopy Techniques and Applications
- 3D Shape Modeling and Analysis
- Auction Theory and Applications
Indian Institute of Technology Kanpur
2006-2025
The University of Tokyo
2022-2024
RIKEN Center for Computational Science
2019-2022
Osaka University
2010-2019
Protein Research Foundation
2014-2019
Southend University Hospital NHS Foundation Trust
2013-2019
Ritsumeikan University
2017
University of Illinois Chicago
2002-2016
Bose Institute
2004-2013
Indian Institute of Technology Indore
2011
Abstract Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare inflammatory disease of unknown cause. 30% patients have anti-neutrophil cytoplasmic antibodies (ANCA) specific for myeloperoxidase (MPO). Here, we describe genome-wide association study in 676 EGPA cases and 6809 controls, that identifies 4 EGPA-associated loci through conventional case-control analysis, additional associations conditional false discovery rate approach. Many variants are also associated asthma six...
Different phylogenetic trees for the same group of species are often produced either by procedures that use diverse optimality criteria or from different genes in study molecular evolution. Comparing these to find their similarities and dissimilarities, i.e. distance, is thus an important issue computational biology. The nearest neighbor interchange distance subtree-transfer two major metrics have been proposed extensively studied reasons. Despite many appealing aspects such as simplicity...
Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present new MD simulation engine named "myPresto/omegagene" that tailored for enhanced conformational sampling methods with non-Ewald electrostatic potential scheme. Our methods, e.g., virtual-system-coupled multi-canonical (V-McMD) method, replace multi-process parallelized run multiple independent runs avoid inter-node communication overhead. In...
A novel enhanced conformational sampling method, virtual‐system‐coupled adaptive umbrella (V‐AUS), was proposed to compute 300‐K free‐energy landscape for flexible molecular docking, where a virtual degrees of freedom introduced control the sampling. This degree interacts with biomolecular system. V‐AUS applied complex formation two disordered amyloid‐β (Aβ 30–35 ) peptides in periodic box filled by an explicit solvent. An interpeptide distance defined as reaction coordinate, along which...
This paper proposes a new and effective approach, named Trifocal SLAM, to address the intensely complex task of SLAM for environments containing different types dynamic objects. These include objects clearly identified as (e.g. cars, humans, etc) well those which are not originally classified yet still in motion (such chairs, boxes etc). is built upon basic structure ORB SLAM2, with additional semantic segmentation thread consistency module. Unlike traditional two-view geometric methods used...
The free-energy landscape of interaction between a medium-sized peptide, endothelin 1 (ET1), and its receptor, human type B receptor (hETB), was computed using multidimensional virtual-system coupled molecular dynamics, which controls the system's motions by introducing multiple reaction coordinates. hETB embedded in lipid bilayer immersed explicit solvent. All molecules were expressed as all-atom models. resultant had five ranges with decreasing ET1-hETB distance: completely dissociative,...
Abstract Like the β‐turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), criterion (involving at i and i+4) is used here to identify α‐turns from database of known protein structures. At least 15 classes have been enumerated based on location in ϕ,ψ space three central (i+1 i+3)—one major being class AAA, where occupy conventional helical backbone torsion angles. However, moving towards C‐terminal end turn, there shift angles more negative ϕ,...
Identification of sequence motifs that favor cis peptide bonds in proteins is important for understanding and designing containing turns mediated by conformations. From 1 H NMR solution studies on short peptides, we show the Pro‐Pro bond Pro‐Pro‐Phe almost equally populates trans isomers, with isomer stabilized a CH⋯π interaction involving terminal Pro Phe. We also Phe over‐represented at positions immediately following known protein structures. Our results demonstrate conformer as...
ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat other shocks. The function of this protein relies on interconversion between different conformations its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses AFM images provide only partial structural information...
The paper studies the computational complexity and approximation algorithms for a new evolutionary distance between multi-chromosomal genomes introduced recently by Ferretti, Nadeau Sankoff. Here, chromosome is represented as set of genes genome collections chromosomes. syntenic two defined minimum number translocations, fusions fissions required to transform one into other. We prove that computing NP-hard give simple algorithm with performance ratio 2. For case when an upper bound d on...