PROTEIN SCAFFOLD MINIMAL SOFTWARE

We report the structure of a Lig-E type DNA ligase bound to the nicked DNA-adenylate reaction intermediate, confirming that complete encirclement is unnecessary for substrate. Malisi C, Schumann M, Toussaint NC et al (2012) Binding pocket optimization by computational protein design. In the present study, we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding.

PROTEIN SCAFFOLD MINIMAL SOFTWARE

Leaver-Fay A, Tyka M, Lewis SM et al (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Rohl CA, Strauss CE, Misura KM, Baker D (2004) Protein structure prediction using Rosetta. Kohlbacher O, Lenhof HP (2000) BALL-rapid software prototyping in computational molecular biology. Huang B, Schroeder M (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Tantillo DJ, Chen J, Houk KN (1998) Theozymes and compuzymes: theoretical models for biological catalysis. Proteins 80: 1078–1094įriedland GD, Linares AJ, Smith CA, Kortemme T (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. Zhang C, Lai L (2012) AutoMatch: target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds. Lei Y, Luo W, Zhu Y (2011) A matching algorithm for catalytic residue site selection in computational enzyme design.

Hornischer K, Blocker H (1996) Grafting of discontinuous sites: a protein modeling strategy. Hearst DP, Cohen FE (1994) GRAFTER: a computational aid for the design of novel proteins. Computer-aided modeling of sites with pre-defined geometry. Hellinga HW, Richards FM (1991) Construction of new ligand binding sites in proteins of known structure. Malisi C, Kohlbacher O, Höcker B (2009) Automated scaffold selection for enzyme design. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA et al (2006) New algorithms and an in silico benchmark for computational enzyme design.

Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J et al (2008) Kemp elimination catalysts by computational enzyme design. Inhibitor-2 (I-2) is a prototypic inhibitor of protein phosphatase-1 (PP1), a major serine-threonine phosphatase which plays a critical role in synaptic functions (Foley et al., 2021b).The mechanism of inhibition of PP1 by I-2 has been extensively studied in vitro for decades since its purification in 1976 (Cohen, 1989 Lemaire and Bollen, 2020). Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A et al (2008) De novo computational design of retro-aldol enzymes. Pinto AL, Hellinga HW, Caradonna JP (1997) Construction of a catalytically active iron superoxide dismutase by rational protein design.

Protein scaffold minimal