(Q47645695)

4 February 2018

title

Theoretical molecular biology: prospectives and perspectives. (English)

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4 February 2018

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1

R Nussinov

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4 February 2018

language of work or name

English

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publication date

1 March 1987

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4 February 2018

Journal of Theoretical Biology

number of pages

17

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based on heuristic

inferred from page(s)

published in

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4 February 2018

volume

125

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4 February 2018

page(s)

219-235

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4 February 2018

issue

2

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4 February 2018

Gene F of bacteriophage phiX174. Correlation of nucleotide sequences from the DNA and amino acid sequences from the gene product.

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A prevalent persistent global nonrandomness that distinguishes coding and non-coding eucaryotic nuclear DNA sequences

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The influence of codon context on genetic code translation

7 January 2021

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Rates of DNA sequence evolution differ between taxonomic groups

7 January 2021

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Mechanics of sequence-dependent stacking of bases in B-DNA

7 January 2021

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Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex

7 January 2021

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An accelerated algorithm for calculating the secondary structure of single stranded RNAs

7 January 2021

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A speculation on the origin of protein synthesis

7 January 2021

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Cyclic AMP receptor protein: role in transcription activation

7 January 2021

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Double-stranded cleavage by cell extracts near recombinational signal sequences of immunoglobulin genes

7 January 2021

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Base sequence and helix structure variation in B and A DNA

7 January 2021

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Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

7 January 2021

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DNA structural variations in the E. coli tyrT promoter

7 January 2021

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Structural specificities of five commonly used DNA nucleases

7 January 2021

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DNA bending and its relation to nucleosome positioning.

7 January 2021

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Efficient algorithms for folding and comparing nucleic acid sequences

7 January 2021

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The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter

7 January 2021

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Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins.

7 January 2021

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The primary structure of rabbit β-globin mRNA as determined from cloned DNA

7 January 2021

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Recognition of protein coding regions in DNA sequences

7 January 2021

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7 January 2021

Fast optimal alignment

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An improved method of testing for evolutionary homology

7 January 2021

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Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli

7 January 2021

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The Diagram, a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences

7 January 2021

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Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries

7 January 2021

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Expected frequencies of codon use as a function of mutation rates and codon fitnesses

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon usage in bacteria: correlation with gene expressivity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon catalog usage is a genome strategy modulated for gene expressivity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Secondary structure of MS2 phage RNA and bias in code word usage

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon usage in muscle genes and liver genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Hydrophobic interactions in the major groove can influence DNA local structure.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Analogous cleavage of DNA by micrococcal nuclease and a 1,10-phenanthroline-cuprous complex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Essential contact residues within SV40 large T antigen binding sites I and II identified by alkylation-interference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Fast Pattern Matching in Strings

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

An efficient string matching algorithm with k differences for nucleotide and amino acid sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Contextual constraints on synonymous codon choice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Interaction of silent and replacement changes in eukaryotic coding sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Sequence-dependent variation in the conformation of DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Use of an 125I-labelled DNA ligand to probe DNA structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The distal transcription signals of the herpesvirus tk gene share a common hexanucleotide control sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Repeating sequences and gene duplication in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Analysis of gene duplication repeats in the myosin rod.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Confidence limits for homology in protein or gene sequences. The c-myc oncogene and adenovirus E1a protein

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

A general method applicable to the search for similarities in the amino acid sequence of two proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Some rules in the ordering of nucleotides in the DNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Efficient algorithms for searching for exact repetition of nucleotide sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

An efficient code searching for sequence homology and DNA duplication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Doublet frequencies in evolutionary distinct groups

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Structural wrinkles and the genomic regulatory sites of eukaryotes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

TGTG, G clustering and other signals near non-mammalian vertebrate mRNA 3' termini: some implications.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Sequence signals which may be required for efficient formation of mRNA 3' termini

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Structural features are as important as sequence homologies in Drosophila heat shock gene upstream regions.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Sequence signals in eukaryotic upstream regions.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The protein products of the myc and myb oncogenes and adenovirus E1a are structurally related

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Minimal Mutation Trees of Sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

On the Theory and Computation of Evolutionary Distances

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The theory and computation of evolutionary distances: Pattern recognition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Selection pressures on codon usage in the complete genome of bacteriophage T7

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Estimation of Secondary Structure in Ribonucleic Acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Sequence-dependent deformational anisotropy of chromatin DNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

A molecular mechanical model to predict the helix twist angles of B-DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The String-to-String Correction Problem

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

The mouse c-abl locus: molecular cloning and characterization.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Pattern recognition in several sequences: consensus and alignment.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon equilibrium I: Testing for homogeneous equilibrium

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Codon equilibrium II: Its use in estimating silent-substitution rates.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

A dynamic programming algorithm for finding alternative RNA secondary structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-5193%2887%2980043-7

10.1016/S0022-5193(87)80043-7

7 January 2021

Identifiers

DOI

1 reference

4 February 2018

PubMed ID

3657210

1 reference

4 February 2018