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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Li W, Godzik A. Li W, et al. Bioinformatics. 2006 Jul 1;22(13):1658-9. doi: 10.1093/bioinformatics/btl158. Epub 2006 May 26. Bioinformatics. 2006. PMID: 16731699
This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-h …
This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying …
Flexible algorithm for direct multiple alignment of protein structures and sequences.
Godzik A, Skolnick J. Godzik A, et al. Comput Appl Biosci. 1994 Dec;10(6):587-96. doi: 10.1093/bioinformatics/10.6.587. Comput Appl Biosci. 1994. PMID: 7704657
The recently described equivalence between the alignment of two proteins and a conformation of a lattice chain on a two-dimensional square lattice is extended to multiple alignments. The search for the optimal multiple alignment between several proteins, whic …
The recently described equivalence between the alignment of two proteins and a conformation of a lattice chain on a two …
De novo and inverse folding predictions of protein structure and dynamics.
Godzik A, Kolinski A, Skolnick J. Godzik A, et al. J Comput Aided Mol Des. 1993 Aug;7(4):397-438. doi: 10.1007/BF02337559. J Comput Aided Mol Des. 1993. PMID: 8229093 Review.
., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and alrea …
., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of grou …
In search of the ideal protein sequence.
Godzik A. Godzik A. Protein Eng. 1995 May;8(5):409-16. doi: 10.1093/protein/8.5.409. Protein Eng. 1995. PMID: 8532661
The inverse of a folding problem is to find the ideal sequence that folds into a particular protein structure. This problem has been addressed using the topology fingerprint-based threading algorithm, capable of calculating a score (energy) of an arbitrary se …
The inverse of a folding problem is to find the ideal sequence that folds into a particular protein structure. This problem ha …
A method for the prediction of surface "U"-turns and transglobular connections in small proteins.
Kolinski A, Skolnick J, Godzik A, Hu WP. Kolinski A, et al. Proteins. 1997 Feb;27(2):290-308. Proteins. 1997. PMID: 9061792
A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, "U" turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single-domain globular proteins has been d
A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, "U" turns,
Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies.
Zhang B, Jaroszewski L, Rychlewski L, Godzik A. Zhang B, et al. Fold Des. 1997;2(5):307-17. doi: 10.1016/S1359-0278(97)00042-4. Fold Des. 1997. PMID: 9377714
The existence of multiple sequence solutions for a given fold has inspired fold prediction methods in which structural information from one protein is used to estimate the energy of another, putatively similar, structure. ...To utilize pair interaction information, special …
The existence of multiple sequence solutions for a given fold has inspired fold prediction methods in which structural information fr …
Secondary structure prediction using segment similarity.
Rychlewski L, Godzik A. Rychlewski L, et al. Protein Eng. 1997 Oct;10(10):1143-53. doi: 10.1093/protein/10.10.1143. Protein Eng. 1997. PMID: 9488139
The similarity definition is optimized using a genetic algorithm and is based on a 21 x 40 similarity matrix, comparing a target sequence with the sequence and burial status of the proteins from the database. The three-state secondary structure prediction acc …
The similarity definition is optimized using a genetic algorithm and is based on a 21 x 40 similarity matrix, comparing a
Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity.
Fetrow JS, Godzik A, Skolnick J. Fetrow JS, et al. J Mol Biol. 1998 Oct 2;282(4):703-11. doi: 10.1006/jmbi.1998.2061. J Mol Biol. 1998. PMID: 9743619
First, the structure of the protein is identified from its sequence using a threading algorithm, which aligns the sequences to the best matching structure in a structural database and extends sequence analysis well beyond the limits of local sequence identity. Then, …
First, the structure of the protein is identified from its sequence using a threading algorithm, which aligns the sequences to the be …
Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family.
Zhang L, Godzik A, Skolnick J, Fetrow JS. Zhang L, et al. Fold Des. 1998;3(6):535-48. doi: 10.1016/s1359-0278(98)00069-8. Fold Des. 1998. PMID: 9889164
The similarities were incorporated into a three-dimensional motif that specifies essential requirements for the enzymatic functions. ...The study further suggests that YHET_ECOLI, a hypothetical protein classified as a member of the UPF0017 family (an unchara …
The similarities were incorporated into a three-dimensional motif that specifies essential requirements for the enzymatic functions. …
Functional insights from structural predictions: analysis of the Escherichia coli genome.
Rychlewski L, Zhang B, Godzik A. Rychlewski L, et al. Protein Sci. 1999 Mar;8(3):614-24. doi: 10.1110/ps.8.3.614. Protein Sci. 1999. PMID: 10091664 Free PMC article.
Close to 30% of the proteins encoded in the E. coli genome can be recognized as homologous to a protein family with known structure. ...Knowing protein structure adds a new dimension to our understanding of its function and the predictions presented here can be used …
Close to 30% of the proteins encoded in the E. coli genome can be recognized as homologous to a protein family with known structure. …
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