cryoEM Refinement Tools
Lead Investigator(s) Barry Honig
Programs and protocols for refining atomic structures — either experimentally determined or computationally constructed — within cryo-electron microscopy (cryoEM) density maps of macromolecular complexes.
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DelPhi
Lead Investigator(s) Barry Honig
Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
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EDGI
Lead Investigator(s) Barry Honig
EDGI (Enhancer Detection using only Genomic Information) identifies large regulatory elements that consist of evolutionarily conserved, order-independent clusters of short conserved motifs.
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Energy Functions
Lead Investigator(s) Barry Honig
Programs for evaluating or comparing protein structure predictions.
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GRASP
Lead Investigator(s) Anthony Nicholls, Barry Honig
A molecular visualization and analysis program useful for displaying and manipulating the surfaces of molecules and their electrostatic properties.
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GRASP2
Lead Investigator(s) Donald Petrey, Barry Honig
An updated version of the GRASP program used for macromolecular structure and surface visualization.
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GRASS
Lead Investigator(s) Barry Honig
A web-based server that exploits many of the features of the GRASP program, providing interactive molecular graphics and quantitative analysis tools with a simple web-based interface.
HMAP
Lead Investigator(s) Barry Honig
A method for hybrid multidimensional alignment of profiles that combines sequence, secondary, and tertiary information in protein structures into profiles to facilitate the detection of remote homologs and perform sequence-to-sequence alignments.
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JACKAL
Lead Investigator(s) Zhexin Xiang, Barry Honig
A collection of programs for the modeling and analysis of protein structures.
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MarkUs
Lead Investigator(s) Barry Honig
A web server that can assist in the assessment of the biochemical function for a given protein structure.
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Model Quality Assessment: Global and Local Quality Assessment of Protein Models
Lead Investigator(s) Barry Honig
Three protocols for model quality assessment (MQA), including direct assessment of local qualities using statistical potentials and two machine learning-based protocols.
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Nest
Lead Investigator(s) Zhexin Xiang, Barry Honig
An algorithm for modeling protein structure based on a sequence-template alignment.
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PredUs
Lead Investigator(s) Barry Honig
A tool for the prediction of protein-protein interfaces based on interface conservation among structurally similar protein neighbors.
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PrePPI
Lead Investigator(s) Barry Honig
A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
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PrISM
Lead Investigator(s) Barry Honig
An integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling.
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Protein-DNA Interface Alignment Software
Lead Investigator(s) Barry Honig
Aligns the interfacial amino acids from two protein-DNA complexes based on the geometric relationship of each amino acid to its local DNA.
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Protein-DNA Modeling Interface Software
Lead Investigator(s) Barry Honig
This program can be used predict the conformation of the sidechains within a protein-DNA binding interface.
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PUDGE
Lead Investigator(s) Barry Honig
An algorithm for the computational prediction of protein structure using sequence homology.
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SCREEN
Lead Investigator(s) Barry Honig
A tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
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SkyBase
Lead Investigator(s) Barry Honig
A database that stores homology models built by SkyLine analysis.
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SkyLine
Lead Investigator(s)
A high-throughput pipeline for homology modeling of protein structures.
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SPIN-PP
Lead Investigator(s) Barry Honig
A database of all protein-protein interfaces present in the Protein Data Bank.
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STING Millennium
Lead Investigator(s) Barry Honig
A web-based suite of programs for the comprehensive and simultaneous analysis of structure and sequence.
SURFace
Lead Investigator(s) Barry Honig
Programs that calculate solvent accessible surface area and curvature-corrected solvent accessible surface area.
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VISTAL
Lead Investigator(s) Barry Honig
A two-dimensional visualization tool for structural alignments.
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