ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins

A Hooke׳s law-based approach to protein folding rate

(2015) Yasser B. Ruiz-Blanco et al.   JOURNAL OF THEORETICAL BIOLOGY

A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL

(2014) Yasser B. Ruiz-Blanco et al.   CHEMICAL PHYSICS LETTERS

Discrete Derivatives for Atom-Pairs as a Novel Graph-Theoretical Invariant for Generating New Molecular Descriptors: Orthogonality, Interpretation and QSARs/QSPRs on Benchmark Databases

(2014) Oscar Martínez-Santiago et al.   Molecular Informatics

Shannon’s, Mutual, Conditional and Joint Entropy Information Indices: Generalization of Global Indices Defined from Local Vertex Invariants

(2013) Stephen Barigye et al.   Current Computer-Aided Drug Design

Global stability of protein folding from an empirical free energy function

(2013) Yasser B. Ruiz-Blanco et al.   JOURNAL OF THEORETICAL BIOLOGY

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets

(2013) Gerard JP van Westen et al.   Journal of Cheminformatics

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

(2013) Gerard JP van Westen et al.   Journal of Cheminformatics

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

(2013) Dong Xu et al.   Scientific Reports

Relations frequency hypermatrices in mutual, conditional, and joint entropy-based information indices

(2012) Stephen J. Barigye et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

(2012) Cheng-Tsung Lu et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and principles of N-linked protein glycosylation

(2011) Flavio Schwarz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

(2011) H. B. Rao et al.   NUCLEIC ACIDS RESEARCH

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of glycosylation sites using random forests

(2008) Stephen E Hamby et al.   BMC BIOINFORMATICS

Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics

(2008) Huixiao Hong et al.   Journal of Chemical Information and Modeling

Novel 2D TOMOCOMD-CARDD molecular descriptors: atom-based stochastic and non-stochastic bilinear indices and their QSPR applications

(2008) Yovani Marrero-Ponce et al.   JOURNAL OF MATHEMATICAL CHEMISTRY

PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition

(2007) Hong-Bin Shen et al.   ANALYTICAL BIOCHEMISTRY