Protein flexibility predictions using graph theory

By Donald J. Jacobs, A. Rader, Leslie A. Kuhn, M. Thorpe. 2001

745 citations recorded by the source corpus.

Subfields: Biomaterials, Materials Chemistry, Molecular Biology

How researchers see this paper

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

In Biomaterials

In Materials Chemistry

In Molecular Biology

Citations in the corpus

AlphaFold2 and its applications in the fields of biology and medicine (2023, methodology): “They used the program Accuracy of NMR Structures Using RCI and Rigidity (ANSURR), which calculates a protein structure’s local rigidity.(74) They compared AF2 predicted structures and those determined by NMR and found that AF2 tends to be more accurate than NMR ensembles.”
Flexible protein-protein docking. (2006, positive): “Structures obtained from flexibility analysis based on the graph theory algorithm FIRST [5], coupled with conformational sampling using ROCK [11], were shown to improve the quality of results for protein docking with both small molecules and peptides [25 ].”
Principles of Flexible Protein-Protein Docking (2008, neutral): “Jacobs et al .65 developed a graph-theory method which analyzes protein flexibility and identifies rigid and flexible substructures.”
The accuracy of protein structures in solution determined by AlphaFold and NMR (2022, methodology): “We recently developed a method called Accuracy of NMR Structures Using RCI and Rigidity (ANSURR) that calculates the local rigidity of a protein structure (Jacobs et al., 2001) and compares it with the local rigidity as measured using a version of the random coil index (Berjanskii and Wishart, 2008)”
Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins (2014, methodology): “There are multiple ways to create a CE including molecular dynamics (MD) and geometrical simulations such as FIRST/FRODA [38–40].”
FATCAT: a web server for flexible structure comparison and structure similarity searching (2004, background): “Most of them, however, treat protein structures as rigid bodies even though it is well known that proteins are ﬂexible and undergo signiﬁcant structural changes as part of their normal function (9–11).”
Flexible structure alignment by chaining aligned fragment pairs allowing twists (2003, background): “We know, however, that proteins are flexible molecules that undergo significant structural changes as part of their normal function (Wuthrich and Wagner, 1978; Schulz and Schirmer, 1979; Bennett and Huber, 1984; Jacobs et al., 2001).”
Dynamic personalities of proteins (2007, background): “, FIRST (floppy inclusion and rigid substructure topography”
Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification (2017, methodology): “The flexibility or rigidity of the CDR-H3 loop backbone was determined by using several extensions 130 of the Pebble Game Algorithm (PG) (40-43) and method FIRST (44); we refer to here as FIRST-PG.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “The rigidity front propagation model combines elements of ‘rigidity propagation’ (Jacobs et al., 2001, 2003; Rader & Brown, 2011) with the ‘frustration front’ concept of Zhuravlev and Papoian (2010), with the dynamic pre-stress of proteins as large as a few 100 pN (Edwards et al., 2012), and is in…”