A5015204242- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- Gene Regulatory Network Analysis
- Machine Learning in Bioinformatics
- Genomics and Chromatin Dynamics
- Cell Adhesion Molecules Research
- RNA and protein synthesis mechanisms
- Cellular Mechanics and Interactions
- Monoclonal and Polyclonal Antibodies Research
- Protein Kinase Regulation and GTPase Signaling
- DNA and Nucleic Acid Chemistry
- Medicinal plant effects and applications
- Photosynthetic Processes and Mechanisms
- Protein purification and stability
- 14-3-3 protein interactions
- Melanoma and MAPK Pathways
- Endoplasmic Reticulum Stress and Disease
- Wnt/β-catenin signaling in development and cancer
- Immune Cell Function and Interaction
- Receptor Mechanisms and Signaling
- DNA Repair Mechanisms
- 3D Printing in Biomedical Research
The Francis Crick Institute
2015-2025
The Honourable Society of Lincoln's Inn
2002-2016
Universitat Politècnica de Catalunya
2013
Cancer Research UK
2007-2013
Barcelona Supercomputing Center
2013
Imperial College London
2002-2006
Abstract Summary: Protein–protein interactions are central to almost all biological functions, and the atomic details of such can yield insights into mechanisms that underlie these functions. We present a web server wraps extends SwarmDock flexible protein–protein docking algorithm. After uploading PDB files binding partners, generates low energy conformations returns ranked list clustered poses their corresponding structures. The user perform full global docking, or focus on particular...
We present the results for CAPRI Round 30, first joint CASP-CAPRI experiment, which brought together experts from protein structure prediction and protein-protein docking communities. The comprised 25 targets amongst those submitted CASP11 experiment of 2014. included mostly homodimers, a few homotetramers, two heterodimers, chains that could readily be modeled using templates Protein Data Bank. On average 24 groups 7 CASP predictions each target, 12 per target participated in scoring...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Mitotic chromosomes were one of the first cell biological structures to be described, yet their molecular architecture remains poorly understood. We have devised a simple biophysical model 300 kb-long nucleosome chain, size budding yeast chromosome, constrained by interactions between binding sites chromosomal condensin complex, key component interphase and mitotic chromosomes. Comparisons computational experimental (4C) interaction maps, other features, allow us predict mode action....
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
Abstract In previous CAPRI rounds (3–5) we showed that using MD‐generated ensembles, as inputs for a rigid‐body docking algorithm, increased our success rate, especially targets exhibiting substantial amounts of induced fit. recent (6–11), cross‐docking was followed by short MD‐based local refinement the subset solutions with lowest interaction energies after minimization. The above approach promising results target 20, where were able to recover 30% native contacts one submitted models....
ABSTRACT Within the crowded, seemingly chaotic environment of cell, proteins are still able to find their binding partners. This is achieved via an ensemble trajectories, which funnel them towards functional sites, funnel. Here, we characterize funnel‐like energy structures on global landscape using time‐homogeneous finite state Markov chain models. These models based idea that transitions can occur between structurally similar docking solutions, with transition probabilities determined by...
ABSTRACT Reliable identification of near‐native poses docked protein–protein complexes is still an unsolved problem. The intrinsic heterogeneity interactions challenging for traditional biophysical or knowledge based potentials and the many false positive binding sites not unusual. Often, ranking protocols are on initial clustering followed by application energy function to rank each cluster according its lowest member. Here, we present approach only one molecular descriptor (e.g., function)...
Cancers, such as squamous cell carcinoma, frequently invade multicellular units. However, these invading units can be organised in a variety of ways, ranging from thin discontinuous strands to thick 'pushing' collectives. Here we employ an integrated experimental and computational approach identify the factors that determine mode collective cancer invasion. We find matrix proteolysis is linked formation wide but has little effect on maximum extent Cell-cell junctions also favour strands, our...
Abstract The formation of specific protein‐protein interactions is often a key to protein's function. During complex formation, each protein component will undergo change in the conformational state, for some these changes are relatively small and reside primarily at sidechain level; however, others may display notable backbone adjustments. One classic problems protein‐docking field be able priori predict extent such changes. In this work, we investigated three protocols find most suitable...
P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream RAS. RAS proteins contribute to activation p110α by interacting directly with its binding domain (RBD), resulting in promotion many cellular such as cell growth, proliferation and survival. Previous work from our lab has highlighted importance p110α/RAS interaction tumour initiation growth. Here we report discovery characterisation cyclic peptide inhibitor (cyclo-CRVLIR) interacts p110α-RBD...
This paper describes the use of a mixture abduction and induction for temporal modeling effects toxins in metabolic networks. Background knowledge is used which network topology functional classes enzymes. background knowledge, represents present state understanding, incomplete. In order to overcome this incompleteness hypotheses are considered consist specific inhibitions enzymes (ground facts) together with general (non-ground) rules predict likely be inhibited by toxin. The foreground...
We present optimisations applied to a bespoke bio-physical molecular dynamics simulation designed investigate chromosome condensation. Our primary focus is on domain-specific algorithmic improvements determining short-range interaction forces between particles, as certain qualities of the render traditional methods less effective. implement tuned versions code for both CPU architectures and modern many-core architecture found in Intel Xeon Phi coprocessor compare their effectiveness. achieve...