Discrete Models of Biopolymers

Discrete Models of Biopolymers (2000)

Cached

Download Links

[www.tbi.univie.ac.at]
[www.tbi.univie.ac.at]

Other Repositories/Bibliography

DBLP

by Peter Schuster , Peter F. Stadler

Citations:

13 - 5 self

BibTeX

@MISC{Schuster00discretemodels,
    author = {Peter Schuster and Peter F. Stadler},
    title = {Discrete Models of Biopolymers},
    year = {2000}
}

Bookmark

OpenURL

Abstract

Discretized models of biopolymer structures can be used not only as approximations of the actual spatial structures but also as a computationally feasible approach to the generic features of the sequence-structure relationships. We review the combinatorics of nucleic acid secondary structures as well as lattice models of proteins, and show how properties such as the existence of extended neutral networks or shape space covering can be explained on this basis.

Citations

1493	Random Graphs - Bollobas - 2001
341	Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure - Mathews, Sabina, et al. - 1999
329	Fast folding and comparison of RNA secondary structures - Hofacker, Fontana, et al. - 1994
320	The quickhull algorithm for convex hulls - Barber, Dobkin, et al. - 1996
233	The equilibrium partition function and base pair binding probabilities for RNA secondary structures - McCaskill - 1990
150	RNA secondary structures and their prediction - Zuker, Sankoff - 1984
145	From sequences to shapes and back: a case study in RNA secondary structures - Schuster, Fontana, et al. - 1994
143	A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics - SantaLucia - 1998
140	On finding all suboptimal foldings of an RNA molecule - Zuker - 1989
136	Smoothness within ruggedness: The role of neutrality in adaptation - Huynen, Stadler, et al. - 1996
132	Principles of Polymer Chemistry - Flory - 1953
132	Introduction to computational biology. Maps, sequences and genomes - Waterman - 1995
123	Algorithms for Loop Matchings - Nussinov, Pieczenik, et al. - 1978
111	Estimation of effective interresidue contact energies from protein crystal-structures - quasi-chemical approximation - Miyazawa, Jernigan - 1985
99	Principles of protein folding: a perspective from simple extract models. Protein Sci 4: 561–602 - KA, Bromberg, et al. - 1995
95	Fast algorithm for predicting the secondary structure of single-stranded RNA - Nussinov, Jacobson - 1980
94	Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins - Sippl - 1990
89	Continuity in evolution: On the nature of transitions - Fontana, Schuster - 1998
88	Asymptotic methods in enumeration - Bender - 1974
88	Complete suboptimal folding of RNA and the stability of secondary structures - Wuchty, Fontana, et al. - 1999
82	Theory for the folding and stability of globular proteins - Dill - 1985
77	MS: RNA secondary structure: A complete mathematical analysis - TF, Waterman - 1978
72	Generic properties of combinatory maps: neutral networks of RNA secondary structures - Reidys, Stadler, et al. - 1997
69	Statistical Mechanics of Chain Molecules - Flory - 1969
68	Improved predictions of secondary structures for RNA - Jaeger, Turner, et al. - 1989
65	Analysis of RNA sequence structure maps by exhaustive enumeration. II. Structure of neutral networks and shape space covering. Monatshefte fur Chemie 127: 375–389 - Gruner, Giegerich, et al. - 1996
61	RNA folding and combinatory landscapes - Fontana, Stadler, et al. - 1992
60	Statistics of RNA secondary structures - Fontana, DAM, et al. - 1993
58	Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications - Unger, Moult - 1993
52	Kinetics of protein folding. A lattice model study of the requirements for folding to the native state - Sali, Shakhnovich, et al. - 1994
52	The computer simulation of RNA folding pathways using a genetic algorithm - Gultyaev, Batenburg, et al. - 1995
51	Secondary structure of single-stranded nucleic acids - Waterman - 1978
51	Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding - Walter, Turner, et al. - 1994
51	Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information - Zuker, Stiegler - 1981
49	Emergence of preferred structures in a simple model of protein folding - Li, Helling, et al. - 1996
49	Neutrality in fitness landscapes - Reidys, Stadler - 2001
49	Shaping space: the possible and the attainable in RNA genotype-phenotype mapping - Fontana, Schuster - 1998
48	Combinatorics of RNA secondary structures - Hofacker, Schuster, et al. - 1998
47	Improved nearest-neighbor parameters for predicting DNA duplex stability - SantaLucia, Allawi, et al. - 1996
47	Recognition of errors in three-dimensional structures of proteins - Sippl - 1993
43	M: Finite populations induce metastability in evolutionary search. Physics Letters A 1997, 229:144–150. 11 van Nimwegen E, Crutchfield JP: Metastable evolutionary dynamics: crossing fitness barriers or escaping via neutral paths - Nimwegen, JP, et al. - 2000
40	Prediction of RNA secondary structure, including pseudoknotting, by computer simulation - Abrahams, Berg, et al. - 1990
36	Statistics of landscapes based on free energies, replication and degredation rate constants of RNA secondary structures - Fontana, Griesmacher, et al. - 1991
35	Sur un problème de configurations et sur les fractions continues - Touchard
34	Theory for protein mutability and biogenesis - Lau, Dill - 1990
33	Linear trees and RNA secondary structure - Schmitt, Waterman - 1994
33	Computational complexity of a problem in molecular structure prediction. Protein Engineering - Ngo, Marks - 1992
32	Some new sequences generalizing the catalan and motzkin numbers - Stein, Waterman - 1979
32	Statistics of RNA melting kinetics - Tacker, Fontana, et al. - 1994
30	Largest random component of a k-cube - Ajtai, Komlós, et al.