Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding

By Yang Zhang, Daisuke Kihara, Jeffrey Skolnick. 2002

153 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

LOMETS: A local meta-threading-server for protein structure prediction (2007, methodology): “In contrast, the conformational space in I-TASSER is searched by the parallel Monte Carlo sampling method (33), the goal of which is to identify the lowest free-energy state by global search.”
I-TASSER: a unified platform for automated protein structure and function prediction (2010, methodology): “The fragment assembly is performed using a modified replica-exchange Monte Carlo simulation techniqu”
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “The structural reassembly simulations are performed by replica-exchange Monte Carlo (REMC) simulations, which are guided by a composite knowledge-based potential (Zhang et al., 2002).”
Protein Structure Prediction: Is It Useful? (2009, methodology): “The authors used a modified replica-exchange Monte Carlo simulation method [46] to search the conformational space, where the improvement of the energy funnel shape is of the key importance for guiding the simulations toward to the native state.”
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 (2017, methodology): “structures and assembled into full-length structural models by a modified REMC simulation procedure.(32) A composite force field,(10,33,34) which combines the distance restraints calculated from the templates”
TOUCHSTONE II: a new approach to ab initio protein structure prediction. (2003, methodology): “In recent work (Zhang et al., 2002), we developed a new parallel hyperbolic sampling (PHS) algorithm to alleviate the problem of ''ergodicity breaking.''”
Template‐based modeling and free modeling by I‐TASSER in CASP7 (2007, methodology): “20 The structure assembly procedure is driven by a modified replica-exchanged Monte Carlo simulation35,36 and the trajectories in low temperature replicas are clustered by SPICKER.”
Ab initio protein structure prediction using chunk-TASSER. (2007, background): “Parallel Hyperbolic Monte Carlo (MC) sampling (PHS) (41) with replica”
Deep-learning contact-map guided protein structure prediction in CASP13 (2019, methodology): “38 A composite force field, which combines the distance restraints obtained from the threading templates with the sequence-based contact restraints (Equation 3) and the inherent knowledge-based energy terms, is used to guide the structural assembly simulations.”
I-TASSER server for protein 3D structure prediction (2008, unknown): “The conformational space is searched by replica-exchange Monte Carlo simulations [ 22 ].”
Toward the solution of the protein structure prediction problem (2021, background): “…addition to constraints from template alignments, TASSER also incorporates several knowledge-based energy terms important for protein folding ( e.g. , hydrogen bonding, secondary structure formation, side-chain contact formation, etc.) to guide its parallel hyperbolic Monte Carlo simulations (102).”
De novo Protein Structure Prediction by Coupling Contact With Distance Profile (2020, methodology): “For example, MC simulated annealing method [42], [43] is widely used in PSP.”
Ab initio modeling of small proteins by iterative TASSER simulations (2007, unknown): “The initial full-length models are submitted to parallelexchange Monte Carlo sampling [32] for assembly/refinement.”