Improving consensus contact prediction via server correlation reduction (2009)
Gao, Xin, Bu, Dongbo, Xu, Jinbo, Li, Ming
Abstract Background Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although...
Finding Compact Structural Motifs in Many Proteins (2009)
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
Abstract. Multiple structural alignment is a fundamental problem in computational biology. Compared with sequence alignment, structural alignment is more powerful in detecting the evolutionary...
T. Tang, J. Xu, M. Li, Thomas Tang, Jinbo Xu, Ming Li
We present a novel method for clustering short protein segments having strong sequencestructure correlations, and demonstrate that these clusters contain useful structural information via two...
Rohit Singh, Jinbo Xu, Bonnie Berger, Rohit Singh, Jinbo Xu, Bonnie Berger
This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and...
Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
Protein structure prediction is one of the most important and difficult problems in computational molecular biology. Protein threading represents one of the most promising techniques for this...
Consensus-based protein structure prediction methods have been proved to be successful in recent CASPs (Critical Assessment of Structure Prediction). By combining several weaker individual servers, a...
Abstract. This article studies the protein side-chain packing problem using the tree-decomposition of a protein structure. To obtain fast and accurate protein side-chain packing, protein structures...
STRUCT2NET: INTEGRATING STRUCTURE INTO PROTEIN-PROTEIN INTERACTION PREDICTION ROHIT SINGH ∗ (2008)
This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and...
Rapid and Accurate Protein Side Chain Prediction Using Local Backbone Information Only (2008)
Jing Zhang, Xin Gao, Jinbo Xu, Ming Li
Abstract. High-accuracy protein structure modeling demands on accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many...
Fragment-HMM: A new approach to protein structure prediction (2008)
Li, Shuai Cheng, Bu, Dongbo, Xu, Jinbo, Li, Ming
We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly,...
Designing succinct structural alphabets (2008)
Li, Shuai Cheng, Bu, Dongbo, Gao, Xin, Xu, Jinbo, Li, Ming
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more...
I hereby declare that I am the sole author of this thesis. I authorize the University of Waterloo to lend this thesis to other institutions or individuals for the purpose of scholarly research.
Speedup LP approach to protein threading by graph reduction (2007)
Abstract. In our protein structure prediction computer program RAPTOR, we have implemented a linear programming (LP) approach to protein threading based on the template contact map graph. Our protein...
A parameterized algorithm for protein structure alignment (2006)
Jinbo Xu, Feng Jiao, Bonnie Berger
Abstract. This paper proposes a parameterized algorithm for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact...
Fast and accurate algorithms for protein side-chain packing (2006)
This paper studies the protein side-chain packing problem using the tree-decomposition of a protein structure. To obtain fast and accurate protein side-chain packing, protein structures are modeled...
A parameterized algorithm for protein structure alignment (2006)
Abstract. This paper proposes a parameterized algorithm for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact...
A tree-decomposition approach to protein structure prediction (2005)
This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction...
Fold recognition by predicted alignment accuracy (2005)
Abstract—One of the key components in protein structure prediction by protein threading technique is to choose the best overall template for a given target sequence after all the optimal...
Fold recognition by predicted alignment accuracy (2005)
One of the key components in protein structure prediction by protein threading technique is to choose the best overall template for a given target sequence after all the optimal sequence-template...
Rapid protein side-chain packing via tree decomposition (2005)
Abstract. This paper proposes a novel tree decomposition based side-chain assignment algorithm, which can obtain the globally optimal solution of the side-chain packing problem very efficiently....
Thomas Tang, Jinbo Xu, Ming Li
We present a novel method for clustering short protein segments having strong sequencestructure correlations, and demonstrate that these clusters contain useful structural information via two...
Thomas Tang, Jinbo Xu, Ming Li
We present a novel method for clustering short protein segments having strong sequencestructure correlations, and demonstrate that these clusters contain useful structural information via two...
Optimizing Multiple Spaced Seeds for Homology Search (2004)
Jinbo Xu, Daniel Brown, Ming Li, Bin Ma
Optimized spaced seeds improve sensitivity and specificity in local homology search. Several authors have shown that multiple seeds can have better sensitivity and specificity than single seeds. We...
Optimizing Multiple Spaced Seeds for Homology Search (2004)
Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma
Abstract. Optimized spaced seeds improve sensitivity and specificity in local homology search [1]. Several authors [1–4] have shown that multiple seeds can have better sensitivity and specificity...
Optimizing Multiple Spaced Seeds for Homology Search (2004)
Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma
Abstract. Optimized spaced seeds improve sensitivity and specificity in localhomology search [1]. Recently, several authors [2-4] have shown that multiple seeds can have better sensitivity and...
Approximation algorithms for NMR spectral peak assignment (2003)
Zhi-zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, ...
We study a constrained bipartite matching problem where the input is a weighted bipartite graph G = (U, V, E), U is a set of vertices following a sequential order, V is another set of vertices...
Assessment of RAPTOR's Linear Programming Approach in CAFASP3 (2003)
We have developed a new algorithm based on the mathematical theory of linear programming (LP) and implemented it in our program RAPTOR. Our new approach provides an elegant formulation of the protein...
Protein Threading by Linear Programming (2003)
Jinbo Xu, Ming Li, Guohui Lin, Dongsup Kim, Ying Xu
this paper investigates the eectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure, we formulate the protein threading problem...
Singh, Rohit, Xu, Jinbo, Berger, Bonnie
Protein–protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete...
Designing succinct structural alphabets
Li, Shuai Cheng, Bu, Dongbo, Gao, Xin, Xu, Jinbo, Li, Ming
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more...
Fragment-HMM: A new approach to protein structure prediction
Li, Shuai Cheng, Bu, Dongbo, Xu, Jinbo, Li, Ming
We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly,...