MONSSTER: a method for folding globular proteins with a small number of distance restraints.

By Jeffrey Skolnick, Andrzej Kolinski, Angel R. Ortiz. 1997

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “Previous work combined a small number of evolutionarily inferred residue contacts with other, structural, sources of information to successfully predict the structure of some smaller proteins, [16,17,18,19].”
Evaluation of residue-residue contact predictions in CASP9 (2011, methodology): “Several algorithms for deriving an approximate structure of a protein from its contact map have been developed,3–7 reaching different levels of accuracy.”
Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field (2012, background): “This is different from the traditional contact predictions from homologous templates55,56 or machine learning,57,58 but provides comparable accuracy for free-modeling targets.”
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. (2004, methodology): “Low-resolution modeling within the MMTSB Tool Set is based on the MONSSTER program [19].”
Protein contact prediction using metagenome sequence data and residual neural networks (2019, unknown): “…Kim et al., 2014; Kosciolek and Jones, 2014; Marks et al., 2011, 2012; Nugent and Jones, 2012; Ortiz et al., 1999; Ovchinnikov et al., 2015, 2016; Sadowski et al., 2011; Skolnick et al., 1997; Sułkowska et al., 2012; Vendruscolo et al., 1997; Weigt et al., 2009; Wu et al., 2011; Yang et al., 2015).”
Recovery of protein structure from contact maps. (1997, background): “The relevant issue, to which considerable effort has been recently devoted [7,8], concerns how small can be the prefactor a, in order to achieve reasonable reconstruction of protein structure from incomplete experimental contact maps.”
Defining an Essence of Structure Determining Residue Contacts in Proteins (2009, background): “For several years, the distance constraints and other stereo chemical and biophysical restraints have been employed in computational restraint-based protein modelling [7–13].”
Predicting drug–protein interaction using quasi-visual question answering system (2019, background): “Previous studies indicated that the distance map can recover protein 3D structures [Skolnick et al., 1997].”
Assessing the accuracy of contact predictions in CASP13 (2019, methodology): “…in assisting protein structure modeling at CASP 11,12,20 but was successfully employed in specific applications, such as folding small proteins, 21 improving statistical pair potentials, 22 selecting models in fold recognition studies, 23 predicting the disulfide bond connectivity in Cys-rich…”
Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8 (2009, background): “11,12 The actual number of reliably predicted contacts necessary to fold a protein de novo depends on the size of the protein, the accuracy of the predictions and the importance of the predicted pair of interactions to the overall fold.”
A distance‐dependent atomic knowledge‐based potential for improved protein structure selection (2001, background): “15 On the other hand, with today’s computer resources, knowledge-based potentials can be quite successful at fold recognition 16–19 and ab initio structure prediction 20,21 see also Proteins special issue, 2000, on CASP3).”