Molecular dynamics: survey of methods for simulating the activity of proteins
The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
Computer-aided antibody design
Recent clinical trials using antibodies with low toxicity and high efficiency have raised
expectations for the development of next-generation protein therapeutics. However, the …
expectations for the development of next-generation protein therapeutics. However, the …
Design of a novel globular protein fold with atomic-level accuracy
A major challenge of computational protein design is the creation of novel proteins with
arbitrarily chosen three-dimensional structures. Here, we used a general computational …
arbitrarily chosen three-dimensional structures. Here, we used a general computational …
Advances in protein structure prediction and de novo protein design: A review
This review provides an exposition to the important problems of (i) structure prediction in
protein folding and (ii) de novo protein design. The recent advances in protein folding are …
protein folding and (ii) de novo protein design. The recent advances in protein folding are …
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
A previously developed computer program for protein design, RosettaDesign, was used to
predict low free energy sequences for nine naturally occurring protein backbones …
predict low free energy sequences for nine naturally occurring protein backbones …
Protein Design is NP-hard
Biologists working in the area of computational protein design have never doubted the
seriousness of the algorithmic challenges that face them in attempting in silico sequence …
seriousness of the algorithmic challenges that face them in attempting in silico sequence …
Automated design of specificity in molecular recognition
JJ Havranek, PB Harbury - nature structural biology, 2003 - nature.com
Specific protein–protein interactions are crucial in signaling networks and for the assembly
of multi-protein complexes, and represent a challenging goal for protein design. Optimizing …
of multi-protein complexes, and represent a challenging goal for protein design. Optimizing …
Paradigms for computational nucleic acid design
The design of DNA and RNA sequences is critical for many endeavors, from DNA
nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the …
nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the …
Energy functions for protein design: adjustment with protein–protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
N Pokala, TM Handel - Journal of molecular biology, 2005 - Elsevier
The development of the EGAD program and energy function for protein design is described.
In contrast to most protein design methods, which require several empirical parameters or …
In contrast to most protein design methods, which require several empirical parameters or …
Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural …
LL Looger, HW Hellinga - Journal of molecular biology, 2001 - Elsevier
The dead-end elimination (DEE) theorems are powerful tools for the combinatorial
optimization of protein side-chain placement in protein design and homology modeling. In …
optimization of protein side-chain placement in protein design and homology modeling. In …