User profiles for K. Karplus
 | Kevin KarplusProfessor of Biomolecular Engineering, University of California, Santa Cruz Verified email at soe.ucsc.edu Cited by 27722 |
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
… These vectors can then be clustered extremely quickly by standard methods such as K-means
or UPGMA. In Clustal Omega, the alignments are then computed using the very accurate …
or UPGMA. In Clustal Omega, the alignments are then computed using the very accurate …
Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
A correct alignment is an essential requirement in homology modeling. Yet in order to
bridge the structural gap between template and target, which may not only involve loop …
bridge the structural gap between template and target, which may not only involve loop …
Hidden Markov models for detecting remote protein homologies.
MOTIVATION: A new hidden Markov model method (SAM-T98) for finding remote homologs
of protein sequences is described and evaluated. The method begins with a single target …
of protein sequences is described and evaluated. The method begins with a single target …
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
… The SAM-T99 HMM procedure was developed by Kevin Karplus and his colleagues at
Santa Cruz. Here we give an outline of the procedure; which is described in detail elsewhere.7 …
Santa Cruz. Here we give an outline of the procedure; which is described in detail elsewhere.7 …
Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision
…, KR Lieberman, H Rashid, CE Lam, K Karplus… - Nature …, 2012 - nature.com
An emerging DNA sequencing technique uses protein or solid-state pores to analyze individual
strands as they are driven in single-file order past a nanoscale sensor 1 , 2 , 3 . However…
strands as they are driven in single-file order past a nanoscale sensor 1 , 2 , 3 . However…
Digital synthesis of plucked-string and drum timbres
K Karplus, A Strong - Computer Music Journal, 1983 - JSTOR
… This was discovered by Kevin Karplus in December 1979. The simplest description of the …
KHz) are described in a separate paper (Karplus and Strong 1983). Jaffe has programmed the …
KHz) are described in a separate paper (Karplus and Strong 1983). Jaffe has programmed the …
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
The sequences of related proteins can diverge beyond the point where their relationship can
be recognised by pairwise sequence comparisons. In attempts to overcome this limitation, …
be recognised by pairwise sequence comparisons. In attempts to overcome this limitation, …
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology
… for the Blocks database (Karplus, 1995a); one pseudocount method, PC-Opt, which is a
single-component Dirichlet density optimized for the Blocks database (Karplus, 1995a); and the …
single-component Dirichlet density optimized for the Blocks database (Karplus, 1995a); and the …
A flexible motif search technique based on generalized profiles
… Kevin Karplus was responsible for establishing fhe exact equivalen& of paths ih HMMs and
alignm&ts in geneialized nrofiles. Nicolas Moeri was resnonsible for the formal hefinition of …
alignm&ts in geneialized nrofiles. Nicolas Moeri was resnonsible for the formal hefinition of …
Classifying G-protein coupled receptors with support vector machines
… a k-class problem. We have chosen the simplest approach to multi-class SVMs by training k
… We used a nine-component mixture, uprior.9comp (Karplus, 1996), reducing the number of …
… We used a nine-component mixture, uprior.9comp (Karplus, 1996), reducing the number of …