A simple physical model for binding energy hot spots in protein–protein complexes

By Tanja Kortemme, David Baker. 2002

817 citations recorded by the source corpus.

Subfields: 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 Materials Chemistry

1. David Baker
2. Jeffrey J. Gray
3. Tanja Kortemme
4. Yang Zhang
5. Jens Meiler
6. Jinbo Xu
7. I. Samish
8. Robin Pearce

In Molecular Biology

1. David Baker
2. Jeffrey J. Gray
3. Tanja Kortemme
4. Yang Zhang
5. Jinbo Xu
6. Jens Meiler
7. I. Samish
8. Burkhard Rost

Citations in the corpus

• Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, background): “However, most of these approaches depend on the availability of prior knowledge and many biologically relevant systems remain out of reach, as additional experimental information is sparse (e.g. membrane proteins, transient interactions and large complexes).”
• A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “…1986; Kihara et al., 2001; Levitt, 1992; Simons et al., 1997; Wu et al., 2007a; Zhao et al., 2008, 2010), docking (Zhang et al., 1997), binding (Kortemme and Baker, 2002; Laurie and Jackson, 2005), mutation study (Gilis and Rooman, 1996, 1997), decoy ranking (Bauer and Beyer, 1994; Casari and…”
• Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, neutral): “First, the “Robetta” server (85, 86) is used to estimate the contribution to the binding free-energy of each interfacial sidechain (ΔΔGres) via computational alanine scanning.”
• Protein–Protein Interaction Hotspots Carved into Sequences (2007, background): “The Baker lab has shown that given a 3-D structure of a protein complex, it is possible to predict the results of alanine scans specifically and accurately [39,40].”
• Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, neutral): “in several studies [15–18].”
• Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. (2003, background): “44 In this work, however, hydrogen bonds are not weighted according to their degree of burial.”
• EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function (2019, result): “We note that the contributions from some terms (such as the electrostatics) are negligible following the parameter optimization, a phenomenon that was also observed by other studies in the ΔΔ G based energy parameterizations [28].”